-bash: ./install.sh: No such file or directory ================================================================================ OpEx: Downloading BWA ================================================================================ URL transformed to HTTPS due to an HSTS policy --2017-04-25 08:52:36-- https://sourceforge.net/projects/bio-bwa/files/bwa-0.5.10.tar.bz2 Resolving sourceforge.net... 216.34.181.60 Connecting to sourceforge.net|216.34.181.60|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://sourceforge.net/projects/bio-bwa/files/bwa-0.5.10.tar.bz2/download [following] --2017-04-25 08:52:40-- https://sourceforge.net/projects/bio-bwa/files/bwa-0.5.10.tar.bz2/download Connecting to sourceforge.net|216.34.181.60|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.10.tar.bz2?r=&ts=1493081563&use_mirror=jaist [following] --2017-04-25 08:52:43-- https://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.10.tar.bz2?r=&ts=1493081563&use_mirror=jaist Resolving downloads.sourceforge.net... 216.34.181.59 Connecting to downloads.sourceforge.net|216.34.181.59|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://jaist.dl.sourceforge.net/project/bio-bwa/bwa-0.5.10.tar.bz2 [following] --2017-04-25 08:52:46-- https://jaist.dl.sourceforge.net/project/bio-bwa/bwa-0.5.10.tar.bz2 Resolving jaist.dl.sourceforge.net... 150.65.7.130, 2001:df0:2ed:feed::feed Connecting to jaist.dl.sourceforge.net|150.65.7.130|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 119829 (117K) [application/octet-stream] Saving to: ‘bwa-0.5.10.tar.bz2’ 0K .......... .......... .......... .......... .......... 42% 65.3K 1s 50K .......... .......... .......... .......... .......... 85% 88.5K 0s 100K .......... ....... 100% 180K=1.4s 2017-04-25 08:52:48 (82.1 KB/s) - ‘bwa-0.5.10.tar.bz2’ saved [119829/119829] x bwa-0.5.10/ x bwa-0.5.10/COPYING x bwa-0.5.10/ChangeLog x bwa-0.5.10/Makefile x bwa-0.5.10/NEWS x bwa-0.5.10/README x bwa-0.5.10/bamlite.c x bwa-0.5.10/bamlite.h x bwa-0.5.10/bntseq.c x bwa-0.5.10/bntseq.h x bwa-0.5.10/bwa.1 x bwa-0.5.10/bwa.txt x bwa-0.5.10/bwape.c x bwa-0.5.10/bwase.c x bwa-0.5.10/bwase.h x bwa-0.5.10/bwaseqio.c x bwa-0.5.10/bwt.c x bwa-0.5.10/bwt.h x bwa-0.5.10/bwt_gen/ x bwa-0.5.10/bwt_lite.c x bwa-0.5.10/bwt_lite.h x bwa-0.5.10/bwtaln.c x bwa-0.5.10/bwtaln.h x bwa-0.5.10/bwtgap.c x bwa-0.5.10/bwtgap.h x bwa-0.5.10/bwtindex.c x bwa-0.5.10/bwtio.c x bwa-0.5.10/bwtmisc.c x bwa-0.5.10/bwtsw2.h x bwa-0.5.10/bwtsw2_aux.c x bwa-0.5.10/bwtsw2_chain.c x bwa-0.5.10/bwtsw2_core.c x bwa-0.5.10/bwtsw2_main.c x bwa-0.5.10/cs2nt.c x bwa-0.5.10/is.c x bwa-0.5.10/khash.h x bwa-0.5.10/kseq.h x bwa-0.5.10/ksort.h x bwa-0.5.10/kstring.c x bwa-0.5.10/kstring.h x bwa-0.5.10/kvec.h x bwa-0.5.10/main.c x bwa-0.5.10/main.h x bwa-0.5.10/qualfa2fq.pl x bwa-0.5.10/simple_dp.c x bwa-0.5.10/solid2fastq.pl x bwa-0.5.10/stdaln.c x bwa-0.5.10/stdaln.h x bwa-0.5.10/utils.c x bwa-0.5.10/utils.h x bwa-0.5.10/xa2multi.pl x bwa-0.5.10/bwt_gen/Makefile x bwa-0.5.10/bwt_gen/QSufSort.c x bwa-0.5.10/bwt_gen/QSufSort.h x bwa-0.5.10/bwt_gen/bwa.txt x bwa-0.5.10/bwt_gen/bwt_gen.c x bwa-0.5.10/bwt_gen/bwt_gen.h ================================================================================ OpEx: Downloading Stampy ================================================================================ --2017-04-25 08:52:48-- http://www.well.ox.ac.uk/bioinformatics/Software/stampy-v1.0.14.1.tgz Resolving www.well.ox.ac.uk... 129.67.44.50 Connecting to www.well.ox.ac.uk|129.67.44.50|:80... connected. 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stampy-1.0.14.1/build/python2.6/plugins/bwa.pyc x stampy-1.0.14.1/build/python2.6/plugins/licensekey.py x stampy-1.0.14.1/build/python2.6/ext/__init__.pyc x stampy-1.0.14.1/build/python2.6/ext/makeconstants.pyc x stampy-1.0.14.1/build/macosx-10.6-universal-2.6-ucs2/c/ x stampy-1.0.14.1/build/macosx-10.6-universal-2.6-ucs2/ext/ x stampy-1.0.14.1/build/macosx-10.6-universal-2.6-ucs2/pyx/ x stampy-1.0.14.1/build/macosx-10.6-universal-2.6-ucs2/pyx/maptools.o x stampy-1.0.14.1/build/macosx-10.6-universal-2.6-ucs2/ext/readalign/ x stampy-1.0.14.1/build/macosx-10.6-universal-2.6-ucs2/c/alignutils.o x stampy-1.0.14.1/build/macosx-10.6-universal-2.6-ucs2/c/maputils.o x stampy-1.0.14.1/build/linux-x86_64-2.7-ucs4/c/ x stampy-1.0.14.1/build/linux-x86_64-2.7-ucs4/ext/ x stampy-1.0.14.1/build/linux-x86_64-2.7-ucs4/pyx/ x stampy-1.0.14.1/build/linux-x86_64-2.7-ucs4/pyx/maptools.o x stampy-1.0.14.1/build/linux-x86_64-2.7-ucs4/ext/readalign/ x stampy-1.0.14.1/build/linux-x86_64-2.7-ucs4/c/alignutils.o x stampy-1.0.14.1/build/linux-x86_64-2.7-ucs4/c/maputils.o x stampy-1.0.14.1/build/linux-x86_64-2.7-ucs2/c/ x stampy-1.0.14.1/build/linux-x86_64-2.7-ucs2/ext/ x stampy-1.0.14.1/build/linux-x86_64-2.7-ucs2/pyx/ x stampy-1.0.14.1/build/linux-x86_64-2.7-ucs2/pyx/maptools.o x stampy-1.0.14.1/build/linux-x86_64-2.7-ucs2/ext/readalign/ x stampy-1.0.14.1/build/linux-x86_64-2.7-ucs2/c/alignutils.o x stampy-1.0.14.1/build/linux-x86_64-2.7-ucs2/c/maputils.o x stampy-1.0.14.1/build/linux-x86_64-2.6-ucs4/c/ x stampy-1.0.14.1/build/linux-x86_64-2.6-ucs4/ext/ x stampy-1.0.14.1/build/linux-x86_64-2.6-ucs4/pyx/ x stampy-1.0.14.1/build/linux-x86_64-2.6-ucs4/pyx/maptools.o x stampy-1.0.14.1/build/linux-x86_64-2.6-ucs4/ext/readalign/ x stampy-1.0.14.1/build/linux-x86_64-2.6-ucs4/c/alignutils.o x stampy-1.0.14.1/build/linux-x86_64-2.6-ucs4/c/maputils.o x stampy-1.0.14.1/build/linux-x86_64-2.6-ucs2/c/ x stampy-1.0.14.1/build/linux-x86_64-2.6-ucs2/ext/ x stampy-1.0.14.1/build/linux-x86_64-2.6-ucs2/pyx/ x stampy-1.0.14.1/build/linux-x86_64-2.6-ucs2/pyx/maptools.o x stampy-1.0.14.1/build/linux-x86_64-2.6-ucs2/ext/readalign/ x stampy-1.0.14.1/build/linux-x86_64-2.6-ucs2/c/alignutils.o x stampy-1.0.14.1/build/linux-x86_64-2.6-ucs2/c/maputils.o ================================================================================ OpEx: Downloading Picard ================================================================================ URL transformed to HTTPS due to an HSTS policy --2017-04-25 08:53:05-- https://sourceforge.net/projects/picard/files/picard-tools/1.48/picard-tools-1.48.zip Resolving sourceforge.net... 216.34.181.60 Connecting to sourceforge.net|216.34.181.60|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://sourceforge.net/projects/picard/files/picard-tools/1.48/picard-tools-1.48.zip/download [following] --2017-04-25 08:53:07-- https://sourceforge.net/projects/picard/files/picard-tools/1.48/picard-tools-1.48.zip/download Connecting to sourceforge.net|216.34.181.60|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://downloads.sourceforge.net/project/picard/picard-tools/1.48/picard-tools-1.48.zip?r=&ts=1493081589&use_mirror=jaist [following] --2017-04-25 08:53:10-- https://downloads.sourceforge.net/project/picard/picard-tools/1.48/picard-tools-1.48.zip?r=&ts=1493081589&use_mirror=jaist Resolving downloads.sourceforge.net... 216.34.181.59 Connecting to downloads.sourceforge.net|216.34.181.59|:443... connected. HTTP request sent, awaiting response... 302 Found Location: https://jaist.dl.sourceforge.net/project/picard/picard-tools/1.48/picard-tools-1.48.zip [following] --2017-04-25 08:53:12-- https://jaist.dl.sourceforge.net/project/picard/picard-tools/1.48/picard-tools-1.48.zip Resolving jaist.dl.sourceforge.net... 150.65.7.130, 2001:df0:2ed:feed::feed Connecting to jaist.dl.sourceforge.net|150.65.7.130|:443... connected. 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3900K .......... .......... .......... .......... .......... 13% 322K 2m57s 3950K .......... .......... .......... .......... .......... 13% 173K 2m56s 4000K .......... .......... .......... .......... .......... 13% 58.0K 2m59s 4050K .......... .......... .......... .......... .......... 13% 12.1M 2m57s 4100K .......... .......... .......... .......... .......... 14% 430K 2m55s 4150K .......... .......... .......... .......... .......... 14% 3.06M 2m52s 4200K .......... .......... .......... .......... .......... 14% 11.5M 2m50s 4250K .......... .......... .......... .......... .......... 14% 217K 2m49s 4300K .......... .......... .......... .......... .......... 14% 296K 2m48s 4350K .......... .......... .......... .......... .......... 14% 310K 2m47s 4400K .......... .......... .......... .......... .......... 15% 196K 2m46s 4450K .......... .......... .......... .......... .......... 15% 60.7K 2m48s 4500K .......... .......... .......... .......... .......... 15% 719K 2m46s 4550K .......... .......... .......... .......... .......... 15% 11.7M 2m44s 4600K .......... .......... .......... .......... .......... 15% 5.37M 2m42s 4650K .......... .......... .......... .......... .......... 15% 11.6M 2m40s 4700K .......... .......... .......... .......... .......... 16% 525K 2m39s 4750K .......... .......... .......... .......... .......... 16% 312K 2m38s 4800K .......... .......... .......... .......... .......... 16% 229K 2m37s 4850K .......... .......... .......... .......... .......... 16% 271K 2m36s 4900K .......... .......... .......... .......... .......... 16% 23.7K 2m44s 4950K .......... .......... .......... .......... .......... 16% 11.6M 2m42s 5000K .......... .......... .......... .......... .......... 17% 11.8M 2m41s 5050K .......... .......... .......... .......... .......... 17% 11.7M 2m39s 5100K .......... .......... .......... .......... .......... 17% 11.7M 2m37s 5150K .......... .......... .......... .......... .......... 17% 11.3M 2m35s 5200K .......... .......... .......... .......... .......... 17% 8.92M 2m33s 5250K .......... .......... .......... .......... .......... 17% 11.1M 2m32s 5300K .......... .......... .......... .......... .......... 18% 10.8M 2m30s 5350K .......... .......... .......... .......... .......... 18% 11.0M 2m28s 5400K .......... .......... .......... .......... .......... 18% 10.8M 2m27s 5450K .......... .......... .......... .......... .......... 18% 14.5M 2m25s 5500K .......... .......... .......... .......... .......... 18% 126K 2m25s 5550K .......... .......... .......... .......... .......... 18% 278K 2m24s 5600K .......... .......... .......... .......... .......... 19% 239K 2m24s 5650K .......... .......... .......... .......... .......... 19% 288K 2m23s 5700K .......... .......... .......... .......... .......... 19% 276K 2m22s 5750K .......... .......... .......... .......... .......... 19% 251K 2m21s 5800K .......... .......... .......... .......... .......... 19% 337K 2m20s 5850K 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.......... .......... .......... .......... .......... 22% 214K 2m10s 6550K .......... .......... .......... .......... .......... 22% 63.4K 2m12s 6600K .......... .......... .......... .......... .......... 22% 483K 2m11s 6650K .......... .......... .......... .......... .......... 22% 1.15M 2m10s 6700K .......... .......... .......... .......... .......... 22% 897K 2m9s 6750K .......... .......... .......... .......... .......... 22% 495K 2m8s 6800K .......... .......... .......... .......... .......... 23% 935K 2m7s 6850K .......... .......... .......... .......... .......... 23% 237K 2m6s 6900K .......... .......... .......... .......... .......... 23% 162K 2m6s 6950K .......... .......... .......... .......... .......... 23% 307K 2m5s 7000K .......... .......... .......... .......... .......... 23% 292K 2m5s 7050K .......... .......... .......... .......... .......... 23% 60.6K 2m6s 7100K .......... .......... .......... .......... .......... 24% 327K 2m6s 7150K .......... .......... .......... .......... .......... 24% 335K 2m5s 7200K .......... .......... .......... .......... .......... 24% 1.83M 2m4s 7250K .......... .......... .......... .......... .......... 24% 11.7M 2m3s 7300K .......... .......... .......... .......... .......... 24% 11.7M 2m2s 7350K .......... .......... .......... .......... .......... 24% 275K 2m1s 7400K .......... .......... .......... .......... .......... 25% 273K 2m1s 7450K .......... .......... .......... .......... .......... 25% 329K 2m0s 7500K .......... .......... .......... .......... .......... 25% 246K 1m59s 7550K .......... .......... .......... .......... .......... 25% 57.1K 2m1s 7600K .......... .......... .......... .......... .......... 25% 284K 2m0s 7650K .......... .......... .......... .......... .......... 25% 414K 2m0s 7700K .......... .......... .......... .......... .......... 26% 11.7M 1m59s 7750K .......... .......... .......... .......... .......... 26% 2.47M 1m58s 7800K .......... .......... 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0s 29600K .......... .......... .. 100% 12.2M=2m27s 2017-04-25 08:55:40 (202 KB/s) - ‘picard-tools-1.48.zip’ saved [30333724/30333724] Archive: picard-tools-1.48.zip creating: picard-tools-1.48/ inflating: picard-tools-1.48/AddOrReplaceReadGroups.jar inflating: picard-tools-1.48/BamIndexStats.jar inflating: picard-tools-1.48/BamToBfq.jar inflating: picard-tools-1.48/BuildBamIndex.jar inflating: picard-tools-1.48/CalculateHsMetrics.jar inflating: picard-tools-1.48/CleanSam.jar inflating: picard-tools-1.48/CollectAlignmentSummaryMetrics.jar inflating: picard-tools-1.48/CollectGcBiasMetrics.jar inflating: picard-tools-1.48/CollectInsertSizeMetrics.jar inflating: picard-tools-1.48/CollectMultipleMetrics.jar inflating: picard-tools-1.48/CollectRnaSeqMetrics.jar inflating: picard-tools-1.48/CompareSAMs.jar inflating: picard-tools-1.48/CreateSequenceDictionary.jar inflating: picard-tools-1.48/DownsampleSam.jar inflating: picard-tools-1.48/EstimateLibraryComplexity.jar inflating: picard-tools-1.48/ExtractIlluminaBarcodes.jar inflating: picard-tools-1.48/ExtractSequences.jar inflating: picard-tools-1.48/FastqToSam.jar inflating: picard-tools-1.48/FixMateInformation.jar inflating: picard-tools-1.48/IlluminaBasecallsToSam.jar inflating: picard-tools-1.48/IntervalListTools.jar inflating: picard-tools-1.48/MarkDuplicates.jar inflating: picard-tools-1.48/MeanQualityByCycle.jar inflating: picard-tools-1.48/MergeBamAlignment.jar inflating: picard-tools-1.48/MergeSamFiles.jar inflating: picard-tools-1.48/NormalizeFasta.jar inflating: picard-tools-1.48/QualityScoreDistribution.jar inflating: picard-tools-1.48/ReorderSam.jar inflating: picard-tools-1.48/ReplaceSamHeader.jar inflating: picard-tools-1.48/RevertSam.jar inflating: picard-tools-1.48/SamFormatConverter.jar inflating: picard-tools-1.48/SamToFastq.jar inflating: picard-tools-1.48/SortSam.jar inflating: picard-tools-1.48/ValidateSamFile.jar inflating: picard-tools-1.48/ViewSam.jar inflating: picard-tools-1.48/picard-1.48.jar inflating: picard-tools-1.48/sam-1.48.jar inflating: snappy-java-1.0.3-rc3-20110610.011644-1.jar ================================================================================ OpEx: Downloading Platypus ================================================================================ --2017-04-25 08:55:40-- http://www.well.ox.ac.uk/bioinformatics/Software/Platypus_0.1.5.tgz Resolving www.well.ox.ac.uk... 129.67.44.50 Connecting to www.well.ox.ac.uk|129.67.44.50|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 1719982 (1.6M) [application/x-gzip] Saving to: ‘Platypus_0.1.5.tgz’ 0K .......... .......... .......... .......... .......... 2% 113K 14s 50K .......... .......... .......... .......... .......... 5% 252K 10s 100K .......... .......... .......... .......... .......... 8% 326K 8s 150K .......... .......... .......... .......... .......... 11% 199K 8s 200K .......... .......... .......... .......... .......... 14% 115K 8s 250K .......... .......... .......... .......... .......... 17% 127K 9s 300K .......... .......... .......... .......... .......... 20% 108K 9s 350K .......... .......... .......... .......... .......... 23% 113K 9s 400K .......... .......... .......... .......... .......... 26% 149K 9s 450K .......... .......... .......... .......... .......... 29% 124K 8s 500K .......... .......... .......... .......... .......... 32% 75.0K 9s 550K .......... .......... .......... .......... .......... 35% 111K 8s 600K .......... 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PlatypusRelease/pysam/samtools/bam2depth.c.pysam.c x PlatypusRelease/pysam/samtools/bgzf.c.pysam.c x PlatypusRelease/pysam/samtools/bam_color.c.pysam.c x PlatypusRelease/pysam/samtools/kstring.c.pysam.c x PlatypusRelease/pysam/setup.cfg x PlatypusRelease/pysam/setup.py x PlatypusRelease/pysam/tabix/ x PlatypusRelease/pysam/tabix/pysam.h x PlatypusRelease/pysam/tabix/kseq.h x PlatypusRelease/pysam/tabix/bedidx.c.pysam.c x PlatypusRelease/pysam/tabix/ksort.h x PlatypusRelease/pysam/tabix/tabix.h x PlatypusRelease/pysam/tabix/knetfile.c.pysam.c x PlatypusRelease/pysam/tabix/knetfile.h x PlatypusRelease/pysam/tabix/bgzf.h x PlatypusRelease/pysam/tabix/bam_endian.h x PlatypusRelease/pysam/tabix/kstring.h x PlatypusRelease/pysam/tabix/index.c.pysam.c x PlatypusRelease/pysam/tabix/khash.h x PlatypusRelease/pysam/tabix/msvc_compat.h x PlatypusRelease/pysam/tabix/bgzip.c.pysam.c x PlatypusRelease/pysam/tabix/bgzf.c.pysam.c x PlatypusRelease/pysam/tabix/kstring.c.pysam.c x PlatypusRelease/pysam/THANKS x PlatypusRelease/pysam/ez_setup.py x PlatypusRelease/pysam/pysam.egg-info/ x PlatypusRelease/pysam/pysam.egg-info/SOURCES.txt x PlatypusRelease/pysam/pysam.egg-info/PKG-INFO x PlatypusRelease/pysam/pysam.egg-info/requires.txt x PlatypusRelease/pysam/pysam.egg-info/dependency_links.txt x PlatypusRelease/pysam/pysam.egg-info/top_level.txt x PlatypusRelease/pysam/pysam.egg-info/not-zip-safe x PlatypusRelease/pysam/ez_setup.pyc x PlatypusRelease/pysam/setuptools-0.6c11-py2.6.egg x PlatypusRelease/setup.py ================================================================================ OpEx: Downloading transcript database ================================================================================ --2017-04-25 08:55:58-- http://www.well.ox.ac.uk/bioinformatics/Software/default_transcripts.zip Resolving www.well.ox.ac.uk... 129.67.44.50 Connecting to www.well.ox.ac.uk|129.67.44.50|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 2018750 (1.9M) [application/zip] Saving to: ‘default_transcripts.zip’ 0K .......... .......... .......... .......... .......... 2% 102K 19s 50K .......... .......... .......... .......... .......... 5% 157K 15s 100K .......... .......... .......... .......... .......... 7% 151K 14s 150K .......... .......... .......... .......... .......... 10% 148K 13s 200K .......... .......... .......... .......... .......... 12% 152K 12s 250K .......... .......... .......... .......... .......... 15% 152K 12s 300K .......... .......... .......... .......... .......... 17% 155K 11s 350K .......... .......... .......... .......... .......... 20% 146K 11s 400K .......... .......... .......... .......... .......... 22% 163K 11s 450K .......... .......... .......... .......... .......... 25% 165K 10s 500K .......... .......... .......... .......... .......... 27% 154K 10s 550K .......... .......... .......... .......... .......... 30% 145K 9s 600K 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.......... . 100% 89.1K=15s 2017-04-25 08:56:13 (135 KB/s) - ‘default_transcripts.zip’ saved [2018750/2018750] Archive: default_transcripts.zip inflating: exome_65_GRCh37.gz inflating: exome_65_GRCh37.gz.tbi ================================================================================ OpEx: Building BWA ================================================================================ make[1]: Nothing to be done for `lib'. gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_gen.c -o bwt_gen.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD QSufSort.c -o QSufSort.o ar -scru libbwtgen.a bwt_gen.o QSufSort.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD utils.c -o utils.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt.c -o bwt.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtio.c -o bwtio.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtaln.c -o bwtaln.o In file included from bwtaln.c:11: In file included from ./bwtaln.h:5: ./bwt.h:95:14: warning: inline function 'bwt_2occ' is not defined [-Wundefined-inline] inline void bwt_2occ(const bwt_t *bwt, bwtint_t k, bwtint_t l, ubyte_t c, bwtint_t *ok, bwtint_t *ol); ^ bwtaln.c:61:4: note: used here bwt_2occ(rbwt, k - 1, l, c, &ok, &ol); ^ 1 warning generated. gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtgap.c -o bwtgap.o In file included from bwtgap.c:4: In file included from ./bwtgap.h:4: ./bwt.h:96:14: warning: inline function 'bwt_2occ4' is not defined [-Wundefined-inline] inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]); ^ bwtgap.c:201:3: note: used here bwt_2occ4(bwt, k - 1, l, cnt_k, cnt_l); // retrieve Occ values ^ 1 warning generated. gcc -c -g -Wall -O2 -DHAVE_PTHREAD is.c -o is.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bntseq.c -o bntseq.o bntseq.c:37:1: warning: unused function 'kseq_rewind' [-Wunused-function] KSEQ_INIT(gzFile, gzread) ^ ./kseq.h:205:2: note: expanded from macro 'KSEQ_INIT' __KSEQ_BASIC(type_t) \ ^ ./kseq.h:137:21: note: expanded from macro '__KSEQ_BASIC' static inline void kseq_rewind(kseq_t *ks) \ ^ 1 warning generated. gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtmisc.c -o bwtmisc.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtindex.c -o bwtindex.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD stdaln.c -o stdaln.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD simple_dp.c -o simple_dp.o simple_dp.c:11:1: warning: unused function 'kseq_rewind' [-Wunused-function] KSEQ_INIT(gzFile, gzread) ^ ./kseq.h:205:2: note: expanded from macro 'KSEQ_INIT' __KSEQ_BASIC(type_t) \ ^ ./kseq.h:137:21: note: expanded from macro '__KSEQ_BASIC' static inline void kseq_rewind(kseq_t *ks) \ ^ 1 warning generated. gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwaseqio.c -o bwaseqio.o bwaseqio.c:8:1: warning: unused function 'kseq_rewind' [-Wunused-function] KSEQ_INIT(gzFile, gzread) ^ ./kseq.h:205:2: note: expanded from macro 'KSEQ_INIT' __KSEQ_BASIC(type_t) \ ^ ./kseq.h:137:21: note: expanded from macro '__KSEQ_BASIC' static inline void kseq_rewind(kseq_t *ks) \ ^ 1 warning generated. gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwase.c -o bwase.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwape.c -o bwape.o bwape.c:24:1: warning: unused function 'kh_clear_64' [-Wunused-function] KHASH_MAP_INIT_INT64(64, poslist_t) ^ ./khash.h:488:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ ./khash.h:160:21: note: expanded from macro 'KHASH_INIT' static inline void kh_clear_##name(kh_##name##_t *h) \ ^ :80:1: note: expanded from here kh_clear_64 ^ bwape.c:24:1: warning: unused function 'kh_get_64' [-Wunused-function] ./khash.h:488:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ ./khash.h:167:24: note: expanded from macro 'KHASH_INIT' static inline khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :83:1: note: expanded from here kh_get_64 ^ bwape.c:24:1: warning: unused function 'kh_del_64' [-Wunused-function] ./khash.h:488:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ ./khash.h:279:21: note: expanded from macro 'KHASH_INIT' static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :94:1: note: expanded from here kh_del_64 ^ 3 warnings generated. gcc -c -g -Wall -O2 -DHAVE_PTHREAD kstring.c -o kstring.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD cs2nt.c -o cs2nt.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_core.c -o bwtsw2_core.o bwtsw2_core.c:12:1: warning: unused function 'kh_del_64' [-Wunused-function] KHASH_MAP_INIT_INT64(64, uint64_t) ^ ./khash.h:488:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ ./khash.h:279:21: note: expanded from macro 'KHASH_INIT' static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :265:1: note: expanded from here kh_del_64 ^ bwtsw2_core.c:202:22: warning: unused function 'time_elapse' [-Wunused-function] static inline double time_elapse(const struct rusage *curr, const struct rusage *last) ^ In file included from bwtsw2_core.c:6: ./bwt_lite.h:22:14: warning: inline function 'bwtl_2occ4' is not defined [-Wundefined-inline] inline void bwtl_2occ4(const bwtl_t *bwt, uint32_t k, uint32_t l, uint32_t cntk[4], uint32_t cntl[4]); ^ bwtsw2_core.c:104:3: note: used here bwtl_2occ4(b, k-1, l, cntk, cntl); ^ In file included from bwtsw2_core.c:7: In file included from ./bwtsw2.h:7: ./bwt.h:96:14: warning: inline function 'bwt_2occ4' is not defined [-Wundefined-inline] inline void bwt_2occ4(const bwt_t *bwt, bwtint_t k, bwtint_t l, bwtint_t cntk[4], bwtint_t cntl[4]); ^ bwtsw2_core.c:529:7: note: used here bwt_2occ4(query, p->qk - 1, p->ql, qcntk, qcntl); ^ 4 warnings generated. gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_main.c -o bwtsw2_main.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_aux.c -o bwtsw2_aux.o bwtsw2_aux.c:18:1: warning: unused function 'kseq_rewind' [-Wunused-function] KSEQ_INIT(gzFile, gzread) ^ ./kseq.h:205:2: note: expanded from macro 'KSEQ_INIT' __KSEQ_BASIC(type_t) \ ^ ./kseq.h:137:21: note: expanded from macro '__KSEQ_BASIC' static inline void kseq_rewind(kseq_t *ks) \ ^ 1 warning generated. gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwt_lite.c -o bwt_lite.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bwtsw2_chain.c -o bwtsw2_chain.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD bamlite.c -o bamlite.o gcc -c -g -Wall -O2 -DHAVE_PTHREAD main.c -o main.o gcc -g -Wall -O2 -DHAVE_PTHREAD utils.o bwt.o bwtio.o bwtaln.o bwtgap.o is.o bntseq.o bwtmisc.o bwtindex.o stdaln.o simple_dp.o bwaseqio.o bwase.o bwape.o kstring.o cs2nt.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o bamlite.o main.o -o bwa -lm -lz -lpthread -Lbwt_gen -lbwtgen Undefined symbols for architecture x86_64: "_bwt_2occ", referenced from: _bwt_match_exact in bwt.o _bwt_match_exact_alt in bwt.o _bwt_cal_width in bwtaln.o "_bwt_2occ4", referenced from: _bwt_match_gap in bwtgap.o _bsw2_core in bwtsw2_core.o "_bwtl_2occ4", referenced from: _bsw2_core in bwtsw2_core.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [bwa] Error 1 ================================================================================ OpEx: Building Stampy ================================================================================ gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -fPIC `python2.7-config --includes` -c ext/readalign/readalign.cc -o build/macosx-10.6-universal-2.7-ucs2/readalign.o error: unable to open output file 'build/macosx-10.6-universal-2.7-ucs2/readalign.o': 'No such file or directory' 1 error generated. make[2]: *** [build/macosx-10.6-universal-2.7-ucs2/readalign.o] Error 1 make[1]: *** [build-stampy] Error 2 make: *** [all] Error 2 ================================================================================ OpEx: Building and installing Platypus ================================================================================ running build running build_py creating build creating build/lib creating build/lib/pyvcf copying pyvcf/__init__.py -> build/lib/pyvcf copying pyvcf/filez.py -> build/lib/pyvcf copying pyvcf/vcf-add-ac.py -> build/lib/pyvcf copying pyvcf/vcf-add-hr.py -> build/lib/pyvcf copying pyvcf/vcf-compare.py -> build/lib/pyvcf copying pyvcf/vcf-concordance.py -> build/lib/pyvcf copying pyvcf/vcf-diff.py -> build/lib/pyvcf copying pyvcf/vcf-extract.py -> build/lib/pyvcf copying pyvcf/vcf.py -> build/lib/pyvcf running build running build_py copying extendedoptparse.py -> build/lib running build running build_py copying window.py -> build/lib running build running build_py copying variantutils.py -> build/lib running build running build_py copying platypusexceptions.py -> build/lib running build running build_py running build running build_py copying runner.py -> build/lib running build running build_ext building 'samtoolsWrapper' extension creating build/temp.macosx-10.6-intel-2.7 creating build/temp.macosx-10.6-intel-2.7/samtools /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtoolsWrapper.c -o build/temp.macosx-10.6-intel-2.7/samtoolsWrapper.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtoolsWrapper.c:12891:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ samtoolsWrapper.c:12900:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ samtoolsWrapper.c:12914:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ samtoolsWrapper.c:640:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ samtoolsWrapper.c:701:32: warning: unused function '__Pyx_PyBoolOrNull_FromLong' [-Wunused-function] static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) { ^ samtoolsWrapper.c:11931:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ samtoolsWrapper.c:12322:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ samtoolsWrapper.c:12341:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ samtoolsWrapper.c:12436:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ samtoolsWrapper.c:12560:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ 10 warnings generated. samtoolsWrapper.c:12891:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ samtoolsWrapper.c:12900:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ samtoolsWrapper.c:12914:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ samtoolsWrapper.c:640:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ samtoolsWrapper.c:701:32: warning: unused function '__Pyx_PyBoolOrNull_FromLong' [-Wunused-function] static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) { ^ samtoolsWrapper.c:11931:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ samtoolsWrapper.c:12322:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ samtoolsWrapper.c:12341:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ samtoolsWrapper.c:12436:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ samtoolsWrapper.c:12560:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ 10 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam_util.c -o build/temp.macosx-10.6-intel-2.7/pysam_util.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 pysam_util.c:34:1: warning: unused function 'kh_init_my_i' [-Wunused-function] KHASH_MAP_INIT_INT(my_i, bam_binlist_t); ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :260:1: note: expanded from here kh_init_my_i ^ pysam_util.c:34:1: warning: unused function 'kh_destroy_my_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :2:1: note: expanded from here kh_destroy_my_i ^ pysam_util.c:34:1: warning: unused function 'kh_clear_my_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :5:1: note: expanded from here kh_clear_my_i ^ pysam_util.c:34:1: warning: unused function 'kh_get_my_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :8:1: note: expanded from here kh_get_my_i ^ pysam_util.c:34:1: warning: unused function 'kh_put_my_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :14:1: note: expanded from here kh_put_my_i ^ pysam_util.c:34:1: warning: unused function 'kh_del_my_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :19:1: note: expanded from here kh_del_my_i ^ 6 warnings generated. pysam_util.c:34:1: warning: unused function 'kh_init_my_i' [-Wunused-function] KHASH_MAP_INIT_INT(my_i, bam_binlist_t); ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :260:1: note: expanded from here kh_init_my_i ^ pysam_util.c:34:1: warning: unused function 'kh_destroy_my_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :2:1: note: expanded from here kh_destroy_my_i ^ pysam_util.c:34:1: warning: unused function 'kh_clear_my_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :5:1: note: expanded from here kh_clear_my_i ^ pysam_util.c:34:1: warning: unused function 'kh_get_my_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :8:1: note: expanded from here kh_get_my_i ^ pysam_util.c:34:1: warning: unused function 'kh_put_my_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :14:1: note: expanded from here kh_put_my_i ^ pysam_util.c:34:1: warning: unused function 'kh_del_my_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :19:1: note: expanded from here kh_del_my_i ^ 6 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_aux.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_aux.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtools/bam_aux.c:5:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :248:1: note: expanded from here kh_clear_s ^ samtools/bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :262:1: note: expanded from here kh_del_s ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function] KHASH_MAP_INIT_STR(r2l, str_p) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :269:1: note: expanded from here kh_init_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :274:1: note: expanded from here kh_destroy_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_clear_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :277:1: note: expanded from here kh_clear_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :280:1: note: expanded from here kh_get_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :286:1: note: expanded from here kh_put_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :3:1: note: expanded from here kh_del_r2l ^ 8 warnings generated. samtools/bam_aux.c:5:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :248:1: note: expanded from here kh_clear_s ^ samtools/bam_aux.c:5:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :262:1: note: expanded from here kh_del_s ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_init_r2l' [-Wunused-function] KHASH_MAP_INIT_STR(r2l, str_p) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :269:1: note: expanded from here kh_init_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :274:1: note: expanded from here kh_destroy_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_clear_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :277:1: note: expanded from here kh_clear_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_get_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :280:1: note: expanded from here kh_get_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_put_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :286:1: note: expanded from here kh_put_r2l ^ samtools/bam_aux.c:6:1: warning: unused function 'kh_del_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :3:1: note: expanded from here kh_del_r2l ^ 8 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_cat.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_cat.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_color.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_color.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_import.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_import.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtools/bam_import.c:18:1: warning: unused function 'kh_clear_ref' [-Wunused-function] KHASH_MAP_INIT_STR(ref, uint64_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :248:1: note: expanded from here kh_clear_ref ^ samtools/bam_import.c:18:1: warning: unused function 'kh_get_ref' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :251:1: note: expanded from here kh_get_ref ^ samtools/bam_import.c:18:1: warning: unused function 'kh_del_ref' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :262:1: note: expanded from here kh_del_ref ^ 3 warnings generated. samtools/bam_import.c:18:1: warning: unused function 'kh_clear_ref' [-Wunused-function] KHASH_MAP_INIT_STR(ref, uint64_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :248:1: note: expanded from here kh_clear_ref ^ samtools/bam_import.c:18:1: warning: unused function 'kh_get_ref' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :251:1: note: expanded from here kh_get_ref ^ samtools/bam_import.c:18:1: warning: unused function 'kh_del_ref' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :262:1: note: expanded from here kh_del_ref ^ 3 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_index.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_index.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtools/bam_index.c:64:1: warning: unused function 'kh_clear_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, bam_binlist_t) ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :262:1: note: expanded from here kh_clear_i ^ samtools/bam_index.c:64:1: warning: unused function 'kh_del_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :276:1: note: expanded from here kh_del_i ^ 2 warnings generated. samtools/bam_index.c:64:1: warning: unused function 'kh_clear_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, bam_binlist_t) ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :262:1: note: expanded from here kh_clear_i ^ samtools/bam_index.c:64:1: warning: unused function 'kh_del_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :276:1: note: expanded from here kh_del_i ^ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_lpileup.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_lpileup.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_maqcns.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_maqcns.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_mate.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_mate.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_md.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_md.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_pileup.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_pileup.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_reheader.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_reheader.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_rmdup.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_rmdup.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtools/bam_rmdup.c:12:1: warning: unused function 'kh_get_pos' [-Wunused-function] KHASH_MAP_INIT_INT64(pos, bam1_p) ^ samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :280:1: note: expanded from here kh_get_pos ^ samtools/bam_rmdup.c:12:1: warning: unused function 'kh_del_pos' [-Wunused-function] samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :11:1: note: expanded from here kh_del_pos ^ samtools/bam_rmdup.c:20:1: warning: unused function 'kh_clear_lib' [-Wunused-function] KHASH_MAP_INIT_STR(lib, lib_aux_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :28:1: note: expanded from here kh_clear_lib ^ samtools/bam_rmdup.c:20:1: warning: unused function 'kh_del_lib' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :42:1: note: expanded from here kh_del_lib ^ 4 warnings generated. samtools/bam_rmdup.c:12:1: warning: unused function 'kh_get_pos' [-Wunused-function] KHASH_MAP_INIT_INT64(pos, bam1_p) ^ samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :280:1: note: expanded from here kh_get_pos ^ samtools/bam_rmdup.c:12:1: warning: unused function 'kh_del_pos' [-Wunused-function] samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :11:1: note: expanded from here kh_del_pos ^ samtools/bam_rmdup.c:20:1: warning: unused function 'kh_clear_lib' [-Wunused-function] KHASH_MAP_INIT_STR(lib, lib_aux_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :28:1: note: expanded from here kh_clear_lib ^ samtools/bam_rmdup.c:20:1: warning: unused function 'kh_del_lib' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :42:1: note: expanded from here kh_del_lib ^ 4 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_rmdupse.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_rmdupse.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtools/bam_rmdupse.c:18:1: warning: unused function 'kh_clear_best' [-Wunused-function] KHASH_MAP_INIT_INT(best, elem_p) ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :130:1: note: expanded from here kh_clear_best ^ samtools/bam_rmdupse.c:18:1: warning: unused function 'kh_get_best' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :133:1: note: expanded from here kh_get_best ^ samtools/bam_rmdupse.c:25:1: warning: unused function 'kh_clear_lib' [-Wunused-function] KHASH_MAP_INIT_STR(lib, lib_aux_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :161:1: note: expanded from here kh_clear_lib ^ samtools/bam_rmdupse.c:25:1: warning: unused function 'kh_del_lib' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :175:1: note: expanded from here kh_del_lib ^ 4 warnings generated. samtools/bam_rmdupse.c:18:1: warning: unused function 'kh_clear_best' [-Wunused-function] KHASH_MAP_INIT_INT(best, elem_p) ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :130:1: note: expanded from here kh_clear_best ^ samtools/bam_rmdupse.c:18:1: warning: unused function 'kh_get_best' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :133:1: note: expanded from here kh_get_best ^ samtools/bam_rmdupse.c:25:1: warning: unused function 'kh_clear_lib' [-Wunused-function] KHASH_MAP_INIT_STR(lib, lib_aux_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :161:1: note: expanded from here kh_clear_lib ^ samtools/bam_rmdupse.c:25:1: warning: unused function 'kh_del_lib' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :175:1: note: expanded from here kh_del_lib ^ 4 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_sort.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_sort.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_stat.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_stat.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_tview.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_tview.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtools/bam_tview.c:418:2: warning: "No curses library is available; tview is disabled." [-W#warnings] #warning "No curses library is available; tview is disabled." ^ 1 warning generated. samtools/bam_tview.c:418:2: warning: "No curses library is available; tview is disabled." [-W#warnings] #warning "No curses library is available; tview is disabled." ^ 1 warning generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bedidx.c -o build/temp.macosx-10.6-intel-2.7/samtools/bedidx.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtools/bedidx.c:20:1: warning: unused function 'kh_clear_reg' [-Wunused-function] KHASH_MAP_INIT_STR(reg, bed_reglist_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :262:1: note: expanded from here kh_clear_reg ^ samtools/bedidx.c:20:1: warning: unused function 'kh_del_reg' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :10:1: note: expanded from here kh_del_reg ^ 2 warnings generated. samtools/bedidx.c:20:1: warning: unused function 'kh_clear_reg' [-Wunused-function] KHASH_MAP_INIT_STR(reg, bed_reglist_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :262:1: note: expanded from here kh_clear_reg ^ samtools/bedidx.c:20:1: warning: unused function 'kh_del_reg' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :10:1: note: expanded from here kh_del_reg ^ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bgzf.c -o build/temp.macosx-10.6-intel-2.7/samtools/bgzf.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtools/bgzf.c:44:1: warning: unused function 'kh_clear_cache' [-Wunused-function] KHASH_MAP_INIT_INT64(cache, cache_t) ^ samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :34:1: note: expanded from here kh_clear_cache ^ 1 warning generated. samtools/bgzf.c:44:1: warning: unused function 'kh_clear_cache' [-Wunused-function] KHASH_MAP_INIT_INT64(cache, cache_t) ^ samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :34:1: note: expanded from here kh_clear_cache ^ 1 warning generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bgzip.c -o build/temp.macosx-10.6-intel-2.7/samtools/bgzip.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/cut_target.c -o build/temp.macosx-10.6-intel-2.7/samtools/cut_target.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/errmod.c -o build/temp.macosx-10.6-intel-2.7/samtools/errmod.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtools/errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare] if (m > m) return -1; ^ 1 warning generated. samtools/errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare] if (m > m) return -1; ^ 1 warning generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/faidx.c -o build/temp.macosx-10.6-intel-2.7/samtools/faidx.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtools/faidx.c:13:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, faidx1_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :194:1: note: expanded from here kh_clear_s ^ samtools/faidx.c:13:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :208:1: note: expanded from here kh_del_s ^ 2 warnings generated. samtools/faidx.c:13:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, faidx1_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :194:1: note: expanded from here kh_clear_s ^ samtools/faidx.c:13:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :208:1: note: expanded from here kh_del_s ^ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/glf.c -o build/temp.macosx-10.6-intel-2.7/samtools/glf.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/kaln.c -o build/temp.macosx-10.6-intel-2.7/samtools/kaln.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/knetfile.c -o build/temp.macosx-10.6-intel-2.7/samtools/knetfile.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/kprobaln.c -o build/temp.macosx-10.6-intel-2.7/samtools/kprobaln.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtools/kprobaln.c:164:20: warning: variable 'Pr' is uninitialized when used here [-Wuninitialized] if (p < 1e-100) Pr += -4.343 * log(p), p = 1.; ^~ samtools/kprobaln.c:78:53: note: initialize the variable 'Pr' to silence this warning int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; ^ = 0 1 warning generated. samtools/kprobaln.c:164:20: warning: variable 'Pr' is uninitialized when used here [-Wuninitialized] if (p < 1e-100) Pr += -4.343 * log(p), p = 1.; ^~ samtools/kprobaln.c:78:53: note: initialize the variable 'Pr' to silence this warning int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; ^ = 0 1 warning generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/kstring.c -o build/temp.macosx-10.6-intel-2.7/samtools/kstring.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/phase.c -o build/temp.macosx-10.6-intel-2.7/samtools/phase.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtools/phase.c:45:1: warning: unused function 'kh_clear_set64' [-Wunused-function] KHASH_SET_INIT_INT64(set64) ^ samtools/khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64' KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :61:1: note: expanded from here kh_clear_set64 ^ samtools/phase.c:45:1: warning: unused function 'kh_del_set64' [-Wunused-function] samtools/khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64' KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :75:1: note: expanded from here kh_del_set64 ^ samtools/phase.c:46:1: warning: unused function 'kh_clear_64' [-Wunused-function] KHASH_MAP_INIT_INT64(64, frag_t) ^ samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :90:1: note: expanded from here kh_clear_64 ^ 3 warnings generated. samtools/phase.c:45:1: warning: unused function 'kh_clear_set64' [-Wunused-function] KHASH_SET_INIT_INT64(set64) ^ samtools/khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64' KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :61:1: note: expanded from here kh_clear_set64 ^ samtools/phase.c:45:1: warning: unused function 'kh_del_set64' [-Wunused-function] samtools/khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64' KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :75:1: note: expanded from here kh_del_set64 ^ samtools/phase.c:46:1: warning: unused function 'kh_clear_64' [-Wunused-function] KHASH_MAP_INIT_INT64(64, frag_t) ^ samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :90:1: note: expanded from here kh_clear_64 ^ 3 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/razf.c -o build/temp.macosx-10.6-intel-2.7/samtools/razf.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/sam.c -o build/temp.macosx-10.6-intel-2.7/samtools/sam.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/sam_header.c -o build/temp.macosx-10.6-intel-2.7/samtools/sam_header.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtools/sam_header.c:9:1: warning: unused function 'kh_clear_str' [-Wunused-function] KHASH_MAP_INIT_STR(str, const char *) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :194:1: note: expanded from here kh_clear_str ^ samtools/sam_header.c:9:1: warning: unused function 'kh_del_str' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :208:1: note: expanded from here kh_del_str ^ 2 warnings generated. samtools/sam_header.c:9:1: warning: unused function 'kh_clear_str' [-Wunused-function] KHASH_MAP_INIT_STR(str, const char *) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :194:1: note: expanded from here kh_clear_str ^ samtools/sam_header.c:9:1: warning: unused function 'kh_del_str' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :208:1: note: expanded from here kh_del_str ^ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/sam_view.c -o build/temp.macosx-10.6-intel-2.7/samtools/sam_view.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtools/sam_view.c:11:1: warning: unused function 'kh_clear_rg' [-Wunused-function] KHASH_SET_INIT_STR(rg) ^ samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :51:1: note: expanded from here kh_clear_rg ^ samtools/sam_view.c:11:1: warning: unused function 'kh_del_rg' [-Wunused-function] samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :65:1: note: expanded from here kh_del_rg ^ 2 warnings generated. samtools/sam_view.c:11:1: warning: unused function 'kh_clear_rg' [-Wunused-function] KHASH_SET_INIT_STR(rg) ^ samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :51:1: note: expanded from here kh_clear_rg ^ samtools/sam_view.c:11:1: warning: unused function 'kh_del_rg' [-Wunused-function] samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :65:1: note: expanded from here kh_del_rg ^ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/sample.c -o build/temp.macosx-10.6-intel-2.7/samtools/sample.o -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -msse2 samtools/sample.c:5:1: warning: unused function 'kh_clear_sm' [-Wunused-function] KHASH_MAP_INIT_STR(sm, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :175:1: note: expanded from here kh_clear_sm ^ samtools/sample.c:5:1: warning: unused function 'kh_del_sm' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :189:1: note: expanded from here kh_del_sm ^ 2 warnings generated. samtools/sample.c:5:1: warning: unused function 'kh_clear_sm' [-Wunused-function] KHASH_MAP_INIT_STR(sm, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :175:1: note: expanded from here kh_clear_sm ^ samtools/sample.c:5:1: warning: unused function 'kh_del_sm' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :189:1: note: expanded from here kh_del_sm ^ 2 warnings generated. creating build/lib.macosx-10.6-intel-2.7 /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/samtoolsWrapper.o build/temp.macosx-10.6-intel-2.7/pysam_util.o build/temp.macosx-10.6-intel-2.7/samtools/bam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_aux.o build/temp.macosx-10.6-intel-2.7/samtools/bam_cat.o build/temp.macosx-10.6-intel-2.7/samtools/bam_color.o build/temp.macosx-10.6-intel-2.7/samtools/bam_import.o build/temp.macosx-10.6-intel-2.7/samtools/bam_index.o build/temp.macosx-10.6-intel-2.7/samtools/bam_lpileup.o build/temp.macosx-10.6-intel-2.7/samtools/bam_maqcns.o build/temp.macosx-10.6-intel-2.7/samtools/bam_mate.o build/temp.macosx-10.6-intel-2.7/samtools/bam_md.o build/temp.macosx-10.6-intel-2.7/samtools/bam_pileup.o build/temp.macosx-10.6-intel-2.7/samtools/bam_reheader.o build/temp.macosx-10.6-intel-2.7/samtools/bam_rmdup.o build/temp.macosx-10.6-intel-2.7/samtools/bam_rmdupse.o build/temp.macosx-10.6-intel-2.7/samtools/bam_sort.o build/temp.macosx-10.6-intel-2.7/samtools/bam_stat.o build/temp.macosx-10.6-intel-2.7/samtools/bam_tview.o build/temp.macosx-10.6-intel-2.7/samtools/bedidx.o build/temp.macosx-10.6-intel-2.7/samtools/bgzf.o build/temp.macosx-10.6-intel-2.7/samtools/bgzip.o build/temp.macosx-10.6-intel-2.7/samtools/cut_target.o build/temp.macosx-10.6-intel-2.7/samtools/errmod.o build/temp.macosx-10.6-intel-2.7/samtools/faidx.o build/temp.macosx-10.6-intel-2.7/samtools/glf.o build/temp.macosx-10.6-intel-2.7/samtools/kaln.o build/temp.macosx-10.6-intel-2.7/samtools/knetfile.o build/temp.macosx-10.6-intel-2.7/samtools/kprobaln.o build/temp.macosx-10.6-intel-2.7/samtools/kstring.o build/temp.macosx-10.6-intel-2.7/samtools/phase.o build/temp.macosx-10.6-intel-2.7/samtools/razf.o build/temp.macosx-10.6-intel-2.7/samtools/sam.o build/temp.macosx-10.6-intel-2.7/samtools/sam_header.o build/temp.macosx-10.6-intel-2.7/samtools/sam_view.o build/temp.macosx-10.6-intel-2.7/samtools/sample.o -lz -o build/lib.macosx-10.6-intel-2.7/samtoolsWrapper.so building 'fastafile' extension /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c fastafile.c -o build/temp.macosx-10.6-intel-2.7/fastafile.o -msse2 fastafile.c:4775:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ fastafile.c:4784:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ fastafile.c:4798:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ fastafile.c:459:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { ^ fastafile.c:479:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ fastafile.c:3981:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ fastafile.c:4058:27: warning: unused function '__Pyx_ErrFetch' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { ^ fastafile.c:4204:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ fastafile.c:4223:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ fastafile.c:4242:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ fastafile.c:4261:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ fastafile.c:4280:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ fastafile.c:4318:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ fastafile.c:4337:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ fastafile.c:4356:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ fastafile.c:4375:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ fastafile.c:4569:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 17 warnings generated. fastafile.c:4775:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ fastafile.c:4784:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ fastafile.c:4798:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ fastafile.c:459:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { ^ fastafile.c:479:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ fastafile.c:3981:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ fastafile.c:4058:27: warning: unused function '__Pyx_ErrFetch' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { ^ fastafile.c:4204:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ fastafile.c:4223:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ fastafile.c:4242:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ fastafile.c:4261:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ fastafile.c:4280:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ fastafile.c:4318:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ fastafile.c:4337:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ fastafile.c:4356:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ fastafile.c:4375:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ fastafile.c:4569:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 17 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/fastafile.o -o build/lib.macosx-10.6-intel-2.7/fastafile.so building 'bamfileutils' extension /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c bamfileutils.c -o build/temp.macosx-10.6-intel-2.7/bamfileutils.o -msse2 bamfileutils.c:3090:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ bamfileutils.c:5020:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ bamfileutils.c:5609:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ bamfileutils.c:8282:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ bamfileutils.c:8291:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ bamfileutils.c:8305:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ bamfileutils.c:7333:27: warning: unused function '__Pyx_ErrFetch' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { ^ bamfileutils.c:785:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { ^ bamfileutils.c:805:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ bamfileutils.c:7498:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ bamfileutils.c:7559:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ bamfileutils.c:7578:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ bamfileutils.c:7597:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ bamfileutils.c:7616:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ bamfileutils.c:7635:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ bamfileutils.c:7673:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ bamfileutils.c:7692:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ bamfileutils.c:7711:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ bamfileutils.c:7730:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ bamfileutils.c:7854:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ bamfileutils.c:7924:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 21 warnings generated. bamfileutils.c:3090:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ bamfileutils.c:5020:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ bamfileutils.c:5609:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ bamfileutils.c:8282:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ bamfileutils.c:8291:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ bamfileutils.c:8305:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ bamfileutils.c:7333:27: warning: unused function '__Pyx_ErrFetch' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { ^ bamfileutils.c:785:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { ^ bamfileutils.c:805:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ bamfileutils.c:7498:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ bamfileutils.c:7559:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ bamfileutils.c:7578:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ bamfileutils.c:7597:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ bamfileutils.c:7616:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ bamfileutils.c:7635:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ bamfileutils.c:7673:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ bamfileutils.c:7692:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ bamfileutils.c:7711:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ bamfileutils.c:7730:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ bamfileutils.c:7854:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ bamfileutils.c:7924:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 21 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/bamfileutils.o -o build/lib.macosx-10.6-intel-2.7/bamfileutils.so building 'variant' extension /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c variant.c -o build/temp.macosx-10.6-intel-2.7/variant.o -msse2 variant.c:9661:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ variant.c:9670:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ variant.c:9684:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ variant.c:8871:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ variant.c:8920:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ variant.c:8939:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ variant.c:8958:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ variant.c:8977:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ variant.c:8996:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ variant.c:9034:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ variant.c:9053:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ variant.c:9072:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ variant.c:9091:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ variant.c:9215:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ variant.c:9285:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 15 warnings generated. variant.c:9661:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ variant.c:9670:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ variant.c:9684:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ variant.c:8871:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ variant.c:8920:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ variant.c:8939:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ variant.c:8958:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ variant.c:8977:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ variant.c:8996:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ variant.c:9034:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ variant.c:9053:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ variant.c:9072:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ variant.c:9091:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ variant.c:9215:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ variant.c:9285:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 15 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/variant.o -o build/lib.macosx-10.6-intel-2.7/variant.so building 'cerrormodel' extension /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c cerrormodel.c -o build/temp.macosx-10.6-intel-2.7/cerrormodel.o -msse2 cerrormodel.c:2264:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ cerrormodel.c:2451:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ cerrormodel.c:4064:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ cerrormodel.c:5521:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ cerrormodel.c:5535:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ cerrormodel.c:4567:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ cerrormodel.c:422:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { ^ cerrormodel.c:442:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ cerrormodel.c:497:27: warning: unused function '__Pyx_NegateNonNeg' [-Wunused-function] static CYTHON_INLINE long __Pyx_NegateNonNeg(long b) { return unlikely(b < 0) ? b : !b; } ^ cerrormodel.c:498:32: warning: unused function '__Pyx_PyBoolOrNull_FromLong' [-Wunused-function] static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) { ^ cerrormodel.c:4921:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ cerrormodel.c:4940:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ cerrormodel.c:4959:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ cerrormodel.c:4978:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ cerrormodel.c:4997:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ cerrormodel.c:5035:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ cerrormodel.c:5054:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ cerrormodel.c:5073:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ cerrormodel.c:5092:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ cerrormodel.c:5216:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ cerrormodel.c:5286:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 21 warnings generated. cerrormodel.c:2264:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ cerrormodel.c:2451:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ cerrormodel.c:4064:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ cerrormodel.c:5521:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ cerrormodel.c:5535:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ cerrormodel.c:4567:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ cerrormodel.c:422:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { ^ cerrormodel.c:442:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ cerrormodel.c:497:27: warning: unused function '__Pyx_NegateNonNeg' [-Wunused-function] static CYTHON_INLINE long __Pyx_NegateNonNeg(long b) { return unlikely(b < 0) ? b : !b; } ^ cerrormodel.c:498:32: warning: unused function '__Pyx_PyBoolOrNull_FromLong' [-Wunused-function] static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) { ^ cerrormodel.c:4921:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ cerrormodel.c:4940:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ cerrormodel.c:4959:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ cerrormodel.c:4978:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ cerrormodel.c:4997:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ cerrormodel.c:5035:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ cerrormodel.c:5054:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ cerrormodel.c:5073:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ cerrormodel.c:5092:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ cerrormodel.c:5216:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ cerrormodel.c:5286:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 21 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c tandem.c -o build/temp.macosx-10.6-intel-2.7/tandem.o -msse2 /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/cerrormodel.o build/temp.macosx-10.6-intel-2.7/tandem.o -o build/lib.macosx-10.6-intel-2.7/cerrormodel.so building 'calign' extension /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c calign.c -o build/temp.macosx-10.6-intel-2.7/calign.o -msse2 calign.c:2749:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ calign.c:2758:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ calign.c:2772:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ calign.c:1961:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ calign.c:1980:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ calign.c:1999:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ calign.c:2018:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ calign.c:2037:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ calign.c:2075:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ calign.c:2094:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ calign.c:2113:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ calign.c:2132:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ calign.c:2256:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ calign.c:2326:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 14 warnings generated. calign.c:2749:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ calign.c:2758:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ calign.c:2772:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ calign.c:1961:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ calign.c:1980:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ calign.c:1999:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ calign.c:2018:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ calign.c:2037:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ calign.c:2075:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ calign.c:2094:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ calign.c:2113:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ calign.c:2132:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ calign.c:2256:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ calign.c:2326:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 14 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c align.c -o build/temp.macosx-10.6-intel-2.7/align.o -msse2 /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/calign.o build/temp.macosx-10.6-intel-2.7/align.o -o build/lib.macosx-10.6-intel-2.7/calign.so building 'chaplotype' extension /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I./ -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c chaplotype.c -o build/temp.macosx-10.6-intel-2.7/chaplotype.o -msse2 chaplotype.c:8842:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ chaplotype.c:8851:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ chaplotype.c:8865:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ chaplotype.c:7889:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ chaplotype.c:964:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { ^ chaplotype.c:8064:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ chaplotype.c:8083:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ chaplotype.c:8102:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ chaplotype.c:8121:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ chaplotype.c:8140:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ chaplotype.c:8178:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ chaplotype.c:8197:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ chaplotype.c:8216:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ chaplotype.c:8235:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ chaplotype.c:8429:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 15 warnings generated. chaplotype.c:8842:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ chaplotype.c:8851:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ chaplotype.c:8865:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ chaplotype.c:7889:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ chaplotype.c:964:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { ^ chaplotype.c:8064:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ chaplotype.c:8083:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ chaplotype.c:8102:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ chaplotype.c:8121:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ chaplotype.c:8140:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ chaplotype.c:8178:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ chaplotype.c:8197:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ chaplotype.c:8216:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ chaplotype.c:8235:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ chaplotype.c:8429:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 15 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/chaplotype.o -o build/lib.macosx-10.6-intel-2.7/chaplotype.so building 'cgenotype' extension /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c cgenotype.c -o build/temp.macosx-10.6-intel-2.7/cgenotype.o -msse2 cgenotype.c:3429:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { ^ cgenotype.c:3481:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ cgenotype.c:3490:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ cgenotype.c:3504:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ cgenotype.c:2553:27: warning: unused function '__Pyx_ErrFetch' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { ^ cgenotype.c:992:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ cgenotype.c:1013:32: warning: unused function '__Pyx_GetItemInt_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) { ^ cgenotype.c:2721:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ cgenotype.c:2740:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ cgenotype.c:2759:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ cgenotype.c:2778:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ cgenotype.c:2797:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ cgenotype.c:2835:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ cgenotype.c:2854:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ cgenotype.c:2873:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ cgenotype.c:2892:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ cgenotype.c:3016:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ cgenotype.c:3086:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 18 warnings generated. cgenotype.c:3429:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { ^ cgenotype.c:3481:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ cgenotype.c:3490:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ cgenotype.c:3504:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ cgenotype.c:2553:27: warning: unused function '__Pyx_ErrFetch' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { ^ cgenotype.c:992:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ cgenotype.c:1013:32: warning: unused function '__Pyx_GetItemInt_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i) { ^ cgenotype.c:2721:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ cgenotype.c:2740:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ cgenotype.c:2759:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ cgenotype.c:2778:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ cgenotype.c:2797:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ cgenotype.c:2835:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ cgenotype.c:2854:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ cgenotype.c:2873:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ cgenotype.c:2892:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ cgenotype.c:3016:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ cgenotype.c:3086:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 18 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/cgenotype.o -o build/lib.macosx-10.6-intel-2.7/cgenotype.so building 'cpopulation' extension /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c cpopulation.c -o build/temp.macosx-10.6-intel-2.7/cpopulation.o -msse2 cpopulation.c:1977:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ cpopulation.c:12977:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ cpopulation.c:12986:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ cpopulation.c:13000:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ cpopulation.c:1125:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ cpopulation.c:12101:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ cpopulation.c:1280:32: warning: unused function '__Pyx_PyBoolOrNull_FromLong' [-Wunused-function] static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) { ^ cpopulation.c:12236:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ cpopulation.c:12255:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ cpopulation.c:12274:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ cpopulation.c:12293:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ cpopulation.c:12312:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ cpopulation.c:12350:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ cpopulation.c:12369:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ cpopulation.c:12388:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ cpopulation.c:12407:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ cpopulation.c:12531:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ cpopulation.c:12601:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ cpopulation.c:1882:29: warning: unused function '__pyx_f_11cpopulation_double_min' [-Wunused-function] static CYTHON_INLINE double __pyx_f_11cpopulation_double_min(double __pyx_v_a, double __pyx_v_b) { ^ cpopulation.c:1908:26: warning: unused function '__pyx_f_11cpopulation_int_max' [-Wunused-function] static CYTHON_INLINE int __pyx_f_11cpopulation_int_max(int __pyx_v_a, int __pyx_v_b) { ^ cpopulation.c:1934:26: warning: unused function '__pyx_f_11cpopulation_int_min' [-Wunused-function] static CYTHON_INLINE int __pyx_f_11cpopulation_int_min(int __pyx_v_a, int __pyx_v_b) { ^ 21 warnings generated. cpopulation.c:1977:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ cpopulation.c:12977:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ cpopulation.c:12986:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ cpopulation.c:13000:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ cpopulation.c:1125:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ cpopulation.c:12101:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ cpopulation.c:1280:32: warning: unused function '__Pyx_PyBoolOrNull_FromLong' [-Wunused-function] static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) { ^ cpopulation.c:12236:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ cpopulation.c:12255:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ cpopulation.c:12274:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ cpopulation.c:12293:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ cpopulation.c:12312:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ cpopulation.c:12350:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ cpopulation.c:12369:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ cpopulation.c:12388:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ cpopulation.c:12407:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ cpopulation.c:12531:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ cpopulation.c:12601:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ cpopulation.c:1882:29: warning: unused function '__pyx_f_11cpopulation_double_min' [-Wunused-function] static CYTHON_INLINE double __pyx_f_11cpopulation_double_min(double __pyx_v_a, double __pyx_v_b) { ^ cpopulation.c:1908:26: warning: unused function '__pyx_f_11cpopulation_int_max' [-Wunused-function] static CYTHON_INLINE int __pyx_f_11cpopulation_int_max(int __pyx_v_a, int __pyx_v_b) { ^ cpopulation.c:1934:26: warning: unused function '__pyx_f_11cpopulation_int_min' [-Wunused-function] static CYTHON_INLINE int __pyx_f_11cpopulation_int_min(int __pyx_v_a, int __pyx_v_b) { ^ 21 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/cpopulation.o -o build/lib.macosx-10.6-intel-2.7/cpopulation.so building 'cwindow' extension /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c cwindow.c -o build/temp.macosx-10.6-intel-2.7/cwindow.o -msse2 cwindow.c:4859:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { ^ cwindow.c:4911:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ cwindow.c:4920:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ cwindow.c:4934:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ cwindow.c:3992:27: warning: unused function '__Pyx_ErrFetch' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { ^ cwindow.c:4114:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ cwindow.c:4151:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ cwindow.c:4170:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ cwindow.c:4189:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ cwindow.c:4208:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ cwindow.c:4227:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ cwindow.c:4265:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ cwindow.c:4284:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ cwindow.c:4303:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ cwindow.c:4322:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ cwindow.c:4446:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ cwindow.c:4516:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ cwindow.c:1321:13: warning: unused function '__pyx_f_7cwindow_bisectReadsRight' [-Wunused-function] static int __pyx_f_7cwindow_bisectReadsRight(__pyx_t_15samtoolsWrapper_cAlignedRead **__pyx_v_reads, int __pyx_v_testPos, int __pyx_v_nReads) { ^ 18 warnings generated. cwindow.c:4859:26: warning: unused function '__Pyx_PyObject_IsTrue' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { ^ cwindow.c:4911:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ cwindow.c:4920:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ cwindow.c:4934:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ cwindow.c:3992:27: warning: unused function '__Pyx_ErrFetch' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { ^ cwindow.c:4114:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ cwindow.c:4151:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ cwindow.c:4170:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ cwindow.c:4189:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ cwindow.c:4208:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ cwindow.c:4227:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ cwindow.c:4265:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ cwindow.c:4284:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ cwindow.c:4303:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ cwindow.c:4322:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ cwindow.c:4446:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ cwindow.c:4516:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ cwindow.c:1321:13: warning: unused function '__pyx_f_7cwindow_bisectReadsRight' [-Wunused-function] static int __pyx_f_7cwindow_bisectReadsRight(__pyx_t_15samtoolsWrapper_cAlignedRead **__pyx_v_reads, int __pyx_v_testPos, int __pyx_v_nReads) { ^ 18 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/cwindow.o -o build/lib.macosx-10.6-intel-2.7/cwindow.so building 'cfilter' extension /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c cfilter.c -o build/temp.macosx-10.6-intel-2.7/cfilter.o -msse2 cfilter.c:2665:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ cfilter.c:2674:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ cfilter.c:2688:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ cfilter.c:1922:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ cfilter.c:1941:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ cfilter.c:1960:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ cfilter.c:1979:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ cfilter.c:1998:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ cfilter.c:2017:26: warning: unused function '__Pyx_PyInt_AsInt' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) { ^ cfilter.c:2036:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ cfilter.c:2055:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ cfilter.c:2074:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ cfilter.c:2093:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ cfilter.c:2217:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ cfilter.c:2287:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 15 warnings generated. cfilter.c:2665:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ cfilter.c:2674:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ cfilter.c:2688:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ cfilter.c:1922:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ cfilter.c:1941:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ cfilter.c:1960:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ cfilter.c:1979:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ cfilter.c:1998:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ cfilter.c:2017:26: warning: unused function '__Pyx_PyInt_AsInt' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsInt(PyObject* x) { ^ cfilter.c:2036:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ cfilter.c:2055:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ cfilter.c:2074:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ cfilter.c:2093:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ cfilter.c:2217:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ cfilter.c:2287:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 15 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/cfilter.o -o build/lib.macosx-10.6-intel-2.7/cfilter.so building 'variantFilter' extension /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c variantFilter.c -o build/temp.macosx-10.6-intel-2.7/variantFilter.o -msse2 variantFilter.c:2573:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ variantFilter.c:2582:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ variantFilter.c:2596:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ variantFilter.c:1830:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ variantFilter.c:1849:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ variantFilter.c:1868:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ variantFilter.c:1887:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ variantFilter.c:1906:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ variantFilter.c:1944:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ variantFilter.c:1963:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ variantFilter.c:1982:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ variantFilter.c:2001:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ variantFilter.c:2125:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ variantFilter.c:2195:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 14 warnings generated. variantFilter.c:2573:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ variantFilter.c:2582:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ variantFilter.c:2596:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ variantFilter.c:1830:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ variantFilter.c:1849:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ variantFilter.c:1868:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ variantFilter.c:1887:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ variantFilter.c:1906:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ variantFilter.c:1944:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ variantFilter.c:1963:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ variantFilter.c:1982:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ variantFilter.c:2001:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ variantFilter.c:2125:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ variantFilter.c:2195:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 14 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/variantFilter.o -o build/lib.macosx-10.6-intel-2.7/variantFilter.so building 'variantcaller' extension /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Isamtools -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c variantcaller.c -o build/temp.macosx-10.6-intel-2.7/variantcaller.o -msse2 variantcaller.c:3840:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ variantcaller.c:4067:19: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_v_options = __pyx_v_options; ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~ variantcaller.c:4605:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ variantcaller.c:9874:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ variantcaller.c:9888:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ variantcaller.c:8547:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ variantcaller.c:1222:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ variantcaller.c:8811:27: warning: unused function '__Pyx_ErrFetch' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { ^ variantcaller.c:1297:27: warning: unused function '__Pyx_NegateNonNeg' [-Wunused-function] static CYTHON_INLINE long __Pyx_NegateNonNeg(long b) { return unlikely(b < 0) ? b : !b; } ^ variantcaller.c:1298:32: warning: unused function '__Pyx_PyBoolOrNull_FromLong' [-Wunused-function] static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) { ^ variantcaller.c:9154:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ variantcaller.c:9173:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ variantcaller.c:9192:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ variantcaller.c:9211:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ variantcaller.c:9230:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ variantcaller.c:9268:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ variantcaller.c:9287:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ variantcaller.c:9306:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ variantcaller.c:9325:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ variantcaller.c:9519:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 20 warnings generated. variantcaller.c:3840:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ variantcaller.c:4067:19: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_v_options = __pyx_v_options; ~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~ variantcaller.c:4605:14: warning: explicitly assigning value of variable of type 'PyObject *' (aka 'struct _object *') to itself [-Wself-assign] __pyx_self = __pyx_self; ~~~~~~~~~~ ^ ~~~~~~~~~~ variantcaller.c:9874:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ variantcaller.c:9888:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ variantcaller.c:8547:27: warning: unused function '__Pyx_RaiseNoneIndexingError' [-Wunused-function] static CYTHON_INLINE void __Pyx_RaiseNoneIndexingError(void) { ^ variantcaller.c:1222:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ variantcaller.c:8811:27: warning: unused function '__Pyx_ErrFetch' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { ^ variantcaller.c:1297:27: warning: unused function '__Pyx_NegateNonNeg' [-Wunused-function] static CYTHON_INLINE long __Pyx_NegateNonNeg(long b) { return unlikely(b < 0) ? b : !b; } ^ variantcaller.c:1298:32: warning: unused function '__Pyx_PyBoolOrNull_FromLong' [-Wunused-function] static CYTHON_INLINE PyObject* __Pyx_PyBoolOrNull_FromLong(long b) { ^ variantcaller.c:9154:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ variantcaller.c:9173:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ variantcaller.c:9192:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ variantcaller.c:9211:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ variantcaller.c:9230:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ variantcaller.c:9268:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ variantcaller.c:9287:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ variantcaller.c:9306:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ variantcaller.c:9325:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ variantcaller.c:9519:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 20 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/variantcaller.o -o build/lib.macosx-10.6-intel-2.7/variantcaller.so running install running build running build_py running install_lib creating /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib creating /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7 creating /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib/extendedoptparse.py -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib/platypusexceptions.py -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages creating /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf copying build/lib/pyvcf/__init__.py -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf copying build/lib/pyvcf/filez.py -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf copying build/lib/pyvcf/vcf-add-ac.py -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf copying build/lib/pyvcf/vcf-add-hr.py -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf copying build/lib/pyvcf/vcf-compare.py -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf copying build/lib/pyvcf/vcf-concordance.py -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf copying build/lib/pyvcf/vcf-diff.py -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf copying build/lib/pyvcf/vcf-extract.py -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf copying build/lib/pyvcf/vcf.py -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf copying build/lib/runner.py -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib/variantutils.py -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib/window.py -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages byte-compiling /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/extendedoptparse.py to extendedoptparse.pyc byte-compiling /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/platypusexceptions.py to platypusexceptions.pyc byte-compiling /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf/__init__.py to __init__.pyc byte-compiling /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf/filez.py to filez.pyc byte-compiling /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf/vcf-add-ac.py to vcf-add-ac.pyc byte-compiling /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf/vcf-add-hr.py to vcf-add-hr.pyc byte-compiling /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf/vcf-compare.py to vcf-compare.pyc byte-compiling /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf/vcf-concordance.py to vcf-concordance.pyc byte-compiling /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf/vcf-diff.py to vcf-diff.pyc byte-compiling /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf/vcf-extract.py to vcf-extract.pyc byte-compiling /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf/vcf.py to vcf.pyc byte-compiling /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/runner.py to runner.pyc byte-compiling /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/variantutils.py to variantutils.pyc byte-compiling /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/window.py to window.pyc running install_egg_info Writing /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/pyvcf-0.0.0-py2.7.egg-info running install running build running build_py running install_lib running install_egg_info Writing /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/extendedoptparse-0.0.0-py2.7.egg-info running install running build running build_py running install_lib running install_egg_info Writing /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/window-0.0.0-py2.7.egg-info running install running build running build_py running install_lib running install_egg_info Writing /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/variantutils-0.0.0-py2.7.egg-info running install running build running build_py running install_lib running install_egg_info Writing /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/platypusexceptions-0.0.0-py2.7.egg-info running install running build running build_py running install_lib running install_egg_info Removing /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/extendedoptparse-0.0.0-py2.7.egg-info Writing /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/extendedoptparse-0.0.0-py2.7.egg-info running install running build running build_py running install_lib running install_egg_info Writing /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/runner-0.0.0-py2.7.egg-info running install running build running build_ext running install_lib copying build/lib.macosx-10.6-intel-2.7/bamfileutils.so -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib.macosx-10.6-intel-2.7/calign.so -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib.macosx-10.6-intel-2.7/cerrormodel.so -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib.macosx-10.6-intel-2.7/cfilter.so -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib.macosx-10.6-intel-2.7/cgenotype.so -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib.macosx-10.6-intel-2.7/chaplotype.so -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib.macosx-10.6-intel-2.7/cpopulation.so -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib.macosx-10.6-intel-2.7/cwindow.so -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib.macosx-10.6-intel-2.7/fastafile.so -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib.macosx-10.6-intel-2.7/samtoolsWrapper.so -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib.macosx-10.6-intel-2.7/variant.so -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib.macosx-10.6-intel-2.7/variantcaller.so -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages copying build/lib.macosx-10.6-intel-2.7/variantFilter.so -> /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages running install_egg_info Writing /Users/umdp/Desktop/OpEx-1.0.0/Platypus/lib/python2.7/site-packages/PlatypusCythonModules-0.0.0-py2.7.egg-info ================================================================================ OpEx: Building Pysam ================================================================================ x ./._pysam-0.7.7 x pysam-0.7.7/ x pysam-0.7.7/._.DS_Store x pysam-0.7.7/.DS_Store x pysam-0.7.7/._COPYING x pysam-0.7.7/COPYING x pysam-0.7.7/doc/ x pysam-0.7.7/._get_setuptools.py x pysam-0.7.7/get_setuptools.py x pysam-0.7.7/._INSTALL x pysam-0.7.7/INSTALL x pysam-0.7.7/._KNOWN_BUGS x pysam-0.7.7/KNOWN_BUGS x pysam-0.7.7/._MANIFEST.in x pysam-0.7.7/MANIFEST.in x pysam-0.7.7/._PKG-INFO x pysam-0.7.7/PKG-INFO x pysam-0.7.7/pysam/ x pysam-0.7.7/._pysam.egg-info x pysam-0.7.7/pysam.egg-info/ x pysam-0.7.7/._pysam.py x pysam-0.7.7/pysam.py x pysam-0.7.7/samtools/ x pysam-0.7.7/._setup.cfg x pysam-0.7.7/setup.cfg x pysam-0.7.7/._setup.py x pysam-0.7.7/setup.py x pysam-0.7.7/tabix/ x pysam-0.7.7/tests/ x pysam-0.7.7/._THANKS x pysam-0.7.7/THANKS x pysam-0.7.7/tests/._00README.txt x pysam-0.7.7/tests/00README.txt x pysam-0.7.7/tests/._ex1.fa x pysam-0.7.7/tests/ex1.fa x pysam-0.7.7/tests/._ex1.sam.gz x pysam-0.7.7/tests/ex1.sam.gz x pysam-0.7.7/tests/._ex10.sam x pysam-0.7.7/tests/ex10.sam x pysam-0.7.7/tests/._ex3.sam x pysam-0.7.7/tests/ex3.sam x pysam-0.7.7/tests/._ex4.sam x pysam-0.7.7/tests/ex4.sam x pysam-0.7.7/tests/._ex5.sam x pysam-0.7.7/tests/ex5.sam x pysam-0.7.7/tests/._ex6.sam x pysam-0.7.7/tests/ex6.sam x pysam-0.7.7/tests/._ex7.sam x pysam-0.7.7/tests/ex7.sam x pysam-0.7.7/tests/._ex8.sam x pysam-0.7.7/tests/ex8.sam x pysam-0.7.7/tests/._ex9_fail.bam x pysam-0.7.7/tests/ex9_fail.bam x pysam-0.7.7/tests/._ex9_nofail.bam x pysam-0.7.7/tests/ex9_nofail.bam x pysam-0.7.7/tests/._example.bed.gz x pysam-0.7.7/tests/example.bed.gz x pysam-0.7.7/tests/._example.bed.gz.tbi x pysam-0.7.7/tests/example.bed.gz.tbi x pysam-0.7.7/tests/._example.gtf.gz x pysam-0.7.7/tests/example.gtf.gz x pysam-0.7.7/tests/._example.gtf.gz.tbi x pysam-0.7.7/tests/example.gtf.gz.tbi x pysam-0.7.7/tests/._example.py x pysam-0.7.7/tests/example.py x pysam-0.7.7/tests/._example.vcf40 x pysam-0.7.7/tests/example.vcf40 x pysam-0.7.7/tests/._example_btag.bam x pysam-0.7.7/tests/example_btag.bam x pysam-0.7.7/tests/._example_btag.sam x pysam-0.7.7/tests/example_btag.sam x pysam-0.7.7/tests/._example_empty_header.bam x pysam-0.7.7/tests/example_empty_header.bam x pysam-0.7.7/tests/._example_unmapped_reads_no_sq.sam x pysam-0.7.7/tests/example_unmapped_reads_no_sq.sam x pysam-0.7.7/tests/._example_user_header.sam x pysam-0.7.7/tests/example_user_header.sam x pysam-0.7.7/tests/._issue100.bam x pysam-0.7.7/tests/issue100.bam x pysam-0.7.7/tests/._Makefile x pysam-0.7.7/tests/Makefile x pysam-0.7.7/tests/._pysam_test.py x pysam-0.7.7/tests/pysam_test.py x pysam-0.7.7/tests/._segfault_tests.py x pysam-0.7.7/tests/segfault_tests.py x pysam-0.7.7/tests/._tabix_test.py x pysam-0.7.7/tests/tabix_test.py x pysam-0.7.7/tests/._tag_bug.bam x pysam-0.7.7/tests/tag_bug.bam x pysam-0.7.7/tests/._test_unaligned.bam x pysam-0.7.7/tests/test_unaligned.bam x pysam-0.7.7/tests/vcf-examples/ x pysam-0.7.7/tests/vcf-examples/._10.vcf x pysam-0.7.7/tests/vcf-examples/10.vcf x pysam-0.7.7/tests/vcf-examples/._11.vcf x pysam-0.7.7/tests/vcf-examples/11.vcf x pysam-0.7.7/tests/vcf-examples/._12.vcf x pysam-0.7.7/tests/vcf-examples/12.vcf x pysam-0.7.7/tests/vcf-examples/._13.vcf x pysam-0.7.7/tests/vcf-examples/13.vcf x pysam-0.7.7/tests/vcf-examples/._15.vcf x pysam-0.7.7/tests/vcf-examples/15.vcf x pysam-0.7.7/tests/vcf-examples/._16.vcf x pysam-0.7.7/tests/vcf-examples/16.vcf x pysam-0.7.7/tests/vcf-examples/._18.vcf x pysam-0.7.7/tests/vcf-examples/18.vcf x pysam-0.7.7/tests/vcf-examples/._2.vcf x pysam-0.7.7/tests/vcf-examples/2.vcf x pysam-0.7.7/tests/vcf-examples/._20.vcf x pysam-0.7.7/tests/vcf-examples/20.vcf x pysam-0.7.7/tests/vcf-examples/._21.vcf x pysam-0.7.7/tests/vcf-examples/21.vcf x pysam-0.7.7/tests/vcf-examples/._22.vcf x pysam-0.7.7/tests/vcf-examples/22.vcf x pysam-0.7.7/tests/vcf-examples/._23.vcf x pysam-0.7.7/tests/vcf-examples/23.vcf x pysam-0.7.7/tests/vcf-examples/._24.vcf x pysam-0.7.7/tests/vcf-examples/24.vcf x pysam-0.7.7/tests/vcf-examples/._3.vcf x pysam-0.7.7/tests/vcf-examples/3.vcf x pysam-0.7.7/tests/vcf-examples/._4.vcf x pysam-0.7.7/tests/vcf-examples/4.vcf x pysam-0.7.7/tests/vcf-examples/._5.vcf x pysam-0.7.7/tests/vcf-examples/5.vcf x pysam-0.7.7/tests/vcf-examples/._6.vcf x pysam-0.7.7/tests/vcf-examples/6.vcf x pysam-0.7.7/tests/vcf-examples/._7.vcf x pysam-0.7.7/tests/vcf-examples/7.vcf x pysam-0.7.7/tests/vcf-examples/._8.vcf x pysam-0.7.7/tests/vcf-examples/8.vcf x pysam-0.7.7/tests/vcf-examples/._9.vcf x pysam-0.7.7/tests/vcf-examples/9.vcf x pysam-0.7.7/tests/vcf-examples/._issue85.vcf x pysam-0.7.7/tests/vcf-examples/issue85.vcf x pysam-0.7.7/tabix/.___init__.py x pysam-0.7.7/tabix/__init__.py x pysam-0.7.7/tabix/._bam_endian.h x pysam-0.7.7/tabix/bam_endian.h x pysam-0.7.7/tabix/._bedidx.c x pysam-0.7.7/tabix/bedidx.c x pysam-0.7.7/tabix/._bedidx.c.pysam.c x pysam-0.7.7/tabix/bedidx.c.pysam.c x pysam-0.7.7/tabix/._bgzf.c x pysam-0.7.7/tabix/bgzf.c x pysam-0.7.7/tabix/._bgzf.c.pysam.c x pysam-0.7.7/tabix/bgzf.c.pysam.c x pysam-0.7.7/tabix/._bgzf.h x pysam-0.7.7/tabix/bgzf.h x pysam-0.7.7/tabix/._bgzip.c x pysam-0.7.7/tabix/bgzip.c x pysam-0.7.7/tabix/._bgzip.c.pysam.c x pysam-0.7.7/tabix/bgzip.c.pysam.c x pysam-0.7.7/tabix/._index.c x pysam-0.7.7/tabix/index.c x pysam-0.7.7/tabix/._index.c.pysam.c x pysam-0.7.7/tabix/index.c.pysam.c x pysam-0.7.7/tabix/._khash.h x pysam-0.7.7/tabix/khash.h x pysam-0.7.7/tabix/._knetfile.c x pysam-0.7.7/tabix/knetfile.c x pysam-0.7.7/tabix/._knetfile.c.pysam.c x pysam-0.7.7/tabix/knetfile.c.pysam.c x pysam-0.7.7/tabix/._knetfile.h x pysam-0.7.7/tabix/knetfile.h x pysam-0.7.7/tabix/._kseq.h x pysam-0.7.7/tabix/kseq.h x pysam-0.7.7/tabix/._ksort.h x pysam-0.7.7/tabix/ksort.h x pysam-0.7.7/tabix/._kstring.c x pysam-0.7.7/tabix/kstring.c x pysam-0.7.7/tabix/._kstring.c.pysam.c x pysam-0.7.7/tabix/kstring.c.pysam.c x pysam-0.7.7/tabix/._kstring.h x pysam-0.7.7/tabix/kstring.h x pysam-0.7.7/tabix/._pysam.h x pysam-0.7.7/tabix/pysam.h x pysam-0.7.7/tabix/._tabix.h x pysam-0.7.7/tabix/tabix.h x pysam-0.7.7/samtools/.___init__.py x pysam-0.7.7/samtools/__init__.py x pysam-0.7.7/samtools/._bam.c.pysam.c x pysam-0.7.7/samtools/bam.c.pysam.c x pysam-0.7.7/samtools/._bam.h x pysam-0.7.7/samtools/bam.h x pysam-0.7.7/samtools/._bam2bcf.c.pysam.c x pysam-0.7.7/samtools/bam2bcf.c.pysam.c x pysam-0.7.7/samtools/._bam2bcf.h x pysam-0.7.7/samtools/bam2bcf.h x pysam-0.7.7/samtools/._bam2bcf_indel.c.pysam.c x pysam-0.7.7/samtools/bam2bcf_indel.c.pysam.c x pysam-0.7.7/samtools/._bam2depth.c.pysam.c x pysam-0.7.7/samtools/bam2depth.c.pysam.c x pysam-0.7.7/samtools/._bam_aux.c.pysam.c x pysam-0.7.7/samtools/bam_aux.c.pysam.c x pysam-0.7.7/samtools/._bam_cat.c.pysam.c x pysam-0.7.7/samtools/bam_cat.c.pysam.c x pysam-0.7.7/samtools/._bam_color.c.pysam.c x pysam-0.7.7/samtools/bam_color.c.pysam.c x pysam-0.7.7/samtools/._bam_endian.h x pysam-0.7.7/samtools/bam_endian.h x pysam-0.7.7/samtools/._bam_import.c.pysam.c x pysam-0.7.7/samtools/bam_import.c.pysam.c x pysam-0.7.7/samtools/._bam_index.c.pysam.c x pysam-0.7.7/samtools/bam_index.c.pysam.c x pysam-0.7.7/samtools/._bam_lpileup.c.pysam.c x pysam-0.7.7/samtools/bam_lpileup.c.pysam.c x pysam-0.7.7/samtools/._bam_mate.c.pysam.c x pysam-0.7.7/samtools/bam_mate.c.pysam.c x pysam-0.7.7/samtools/._bam_md.c.pysam.c x pysam-0.7.7/samtools/bam_md.c.pysam.c x pysam-0.7.7/samtools/._bam_pileup.c.pysam.c x pysam-0.7.7/samtools/bam_pileup.c.pysam.c x pysam-0.7.7/samtools/._bam_plcmd.c.pysam.c x pysam-0.7.7/samtools/bam_plcmd.c.pysam.c x pysam-0.7.7/samtools/._bam_reheader.c.pysam.c x pysam-0.7.7/samtools/bam_reheader.c.pysam.c x pysam-0.7.7/samtools/._bam_rmdup.c.pysam.c x pysam-0.7.7/samtools/bam_rmdup.c.pysam.c x pysam-0.7.7/samtools/._bam_rmdupse.c.pysam.c x pysam-0.7.7/samtools/bam_rmdupse.c.pysam.c x pysam-0.7.7/samtools/._bam_sort.c.pysam.c x pysam-0.7.7/samtools/bam_sort.c.pysam.c x pysam-0.7.7/samtools/._bam_stat.c.pysam.c x pysam-0.7.7/samtools/bam_stat.c.pysam.c x pysam-0.7.7/samtools/._bam_tview.c.pysam.c x pysam-0.7.7/samtools/bam_tview.c.pysam.c x pysam-0.7.7/samtools/._bam_tview.h x pysam-0.7.7/samtools/bam_tview.h x pysam-0.7.7/samtools/._bam_tview_curses.c.pysam.c x pysam-0.7.7/samtools/bam_tview_curses.c.pysam.c x pysam-0.7.7/samtools/._bam_tview_html.c.pysam.c x pysam-0.7.7/samtools/bam_tview_html.c.pysam.c x pysam-0.7.7/samtools/._bamshuf.c.pysam.c x pysam-0.7.7/samtools/bamshuf.c.pysam.c x pysam-0.7.7/samtools/bcftools/ x pysam-0.7.7/samtools/._bedcov.c.pysam.c x pysam-0.7.7/samtools/bedcov.c.pysam.c x pysam-0.7.7/samtools/._bedidx.c.pysam.c x pysam-0.7.7/samtools/bedidx.c.pysam.c x pysam-0.7.7/samtools/._bgzf.c.pysam.c x pysam-0.7.7/samtools/bgzf.c.pysam.c x pysam-0.7.7/samtools/._bgzf.h x pysam-0.7.7/samtools/bgzf.h x pysam-0.7.7/samtools/._cut_target.c.pysam.c x pysam-0.7.7/samtools/cut_target.c.pysam.c x pysam-0.7.7/samtools/._errmod.c.pysam.c x pysam-0.7.7/samtools/errmod.c.pysam.c x pysam-0.7.7/samtools/._errmod.h x pysam-0.7.7/samtools/errmod.h x pysam-0.7.7/samtools/._faidx.c.pysam.c x pysam-0.7.7/samtools/faidx.c.pysam.c x pysam-0.7.7/samtools/._faidx.h x pysam-0.7.7/samtools/faidx.h x pysam-0.7.7/samtools/._kaln.c.pysam.c x pysam-0.7.7/samtools/kaln.c.pysam.c x pysam-0.7.7/samtools/._kaln.h x pysam-0.7.7/samtools/kaln.h x pysam-0.7.7/samtools/._khash.h x pysam-0.7.7/samtools/khash.h x pysam-0.7.7/samtools/._klist.h x pysam-0.7.7/samtools/klist.h x pysam-0.7.7/samtools/._knetfile.c.pysam.c x pysam-0.7.7/samtools/knetfile.c.pysam.c x pysam-0.7.7/samtools/._knetfile.h x pysam-0.7.7/samtools/knetfile.h x pysam-0.7.7/samtools/._kprobaln.c.pysam.c x pysam-0.7.7/samtools/kprobaln.c.pysam.c x pysam-0.7.7/samtools/._kprobaln.h x pysam-0.7.7/samtools/kprobaln.h x pysam-0.7.7/samtools/._kseq.h x pysam-0.7.7/samtools/kseq.h x pysam-0.7.7/samtools/._ksort.h x pysam-0.7.7/samtools/ksort.h x pysam-0.7.7/samtools/._kstring.c.pysam.c x pysam-0.7.7/samtools/kstring.c.pysam.c x pysam-0.7.7/samtools/._kstring.h x pysam-0.7.7/samtools/kstring.h x pysam-0.7.7/samtools/misc/ x pysam-0.7.7/samtools/._padding.c.pysam.c x pysam-0.7.7/samtools/padding.c.pysam.c x pysam-0.7.7/samtools/._phase.c.pysam.c x pysam-0.7.7/samtools/phase.c.pysam.c x pysam-0.7.7/samtools/._pysam.h x pysam-0.7.7/samtools/pysam.h x pysam-0.7.7/samtools/._razf.c.pysam.c x pysam-0.7.7/samtools/razf.c.pysam.c x pysam-0.7.7/samtools/._razf.h x pysam-0.7.7/samtools/razf.h x pysam-0.7.7/samtools/._sam.c.pysam.c x pysam-0.7.7/samtools/sam.c.pysam.c x pysam-0.7.7/samtools/._sam.h x pysam-0.7.7/samtools/sam.h x pysam-0.7.7/samtools/._sam_header.c.pysam.c x pysam-0.7.7/samtools/sam_header.c.pysam.c x pysam-0.7.7/samtools/._sam_header.h x pysam-0.7.7/samtools/sam_header.h x pysam-0.7.7/samtools/._sam_view.c.pysam.c x pysam-0.7.7/samtools/sam_view.c.pysam.c x pysam-0.7.7/samtools/._sample.c.pysam.c x pysam-0.7.7/samtools/sample.c.pysam.c x pysam-0.7.7/samtools/._sample.h x pysam-0.7.7/samtools/sample.h x pysam-0.7.7/samtools/win32/ x pysam-0.7.7/samtools/win32/.___init__.py x pysam-0.7.7/samtools/win32/__init__.py x pysam-0.7.7/samtools/win32/._xcurses.h x pysam-0.7.7/samtools/win32/xcurses.h x pysam-0.7.7/samtools/win32/._zconf.h x pysam-0.7.7/samtools/win32/zconf.h x pysam-0.7.7/samtools/win32/._zlib.h x pysam-0.7.7/samtools/win32/zlib.h x pysam-0.7.7/samtools/misc/._ace2sam.c.pysam.c x pysam-0.7.7/samtools/misc/ace2sam.c.pysam.c x pysam-0.7.7/samtools/misc/._md5.c.pysam.c x pysam-0.7.7/samtools/misc/md5.c.pysam.c x pysam-0.7.7/samtools/misc/._md5.h x pysam-0.7.7/samtools/misc/md5.h x pysam-0.7.7/samtools/bcftools/.___init__.py x pysam-0.7.7/samtools/bcftools/__init__.py x pysam-0.7.7/samtools/bcftools/._bcf.c.pysam.c x pysam-0.7.7/samtools/bcftools/bcf.c.pysam.c x pysam-0.7.7/samtools/bcftools/._bcf.h x pysam-0.7.7/samtools/bcftools/bcf.h x pysam-0.7.7/samtools/bcftools/._bcf2qcall.c.pysam.c x pysam-0.7.7/samtools/bcftools/bcf2qcall.c.pysam.c x pysam-0.7.7/samtools/bcftools/._bcfutils.c.pysam.c x pysam-0.7.7/samtools/bcftools/bcfutils.c.pysam.c x pysam-0.7.7/samtools/bcftools/._call1.c.pysam.c x pysam-0.7.7/samtools/bcftools/call1.c.pysam.c x pysam-0.7.7/samtools/bcftools/._em.c.pysam.c x pysam-0.7.7/samtools/bcftools/em.c.pysam.c x pysam-0.7.7/samtools/bcftools/._fet.c.pysam.c x pysam-0.7.7/samtools/bcftools/fet.c.pysam.c x pysam-0.7.7/samtools/bcftools/._index.c.pysam.c x pysam-0.7.7/samtools/bcftools/index.c.pysam.c x pysam-0.7.7/samtools/bcftools/._kfunc.c.pysam.c x pysam-0.7.7/samtools/bcftools/kfunc.c.pysam.c x pysam-0.7.7/samtools/bcftools/._kmin.c.pysam.c x pysam-0.7.7/samtools/bcftools/kmin.c.pysam.c x pysam-0.7.7/samtools/bcftools/._kmin.h x pysam-0.7.7/samtools/bcftools/kmin.h x pysam-0.7.7/samtools/bcftools/._mut.c.pysam.c x pysam-0.7.7/samtools/bcftools/mut.c.pysam.c x pysam-0.7.7/samtools/bcftools/._prob1.c.pysam.c x pysam-0.7.7/samtools/bcftools/prob1.c.pysam.c x pysam-0.7.7/samtools/bcftools/._prob1.h x pysam-0.7.7/samtools/bcftools/prob1.h x pysam-0.7.7/samtools/bcftools/._vcf.c.pysam.c x pysam-0.7.7/samtools/bcftools/vcf.c.pysam.c x pysam-0.7.7/pysam.egg-info/._dependency_links.txt x pysam-0.7.7/pysam.egg-info/dependency_links.txt x pysam-0.7.7/pysam.egg-info/._not-zip-safe x pysam-0.7.7/pysam.egg-info/not-zip-safe x pysam-0.7.7/pysam.egg-info/._PKG-INFO x pysam-0.7.7/pysam.egg-info/PKG-INFO x pysam-0.7.7/pysam.egg-info/._requires.txt x pysam-0.7.7/pysam.egg-info/requires.txt x pysam-0.7.7/pysam.egg-info/._SOURCES.txt x pysam-0.7.7/pysam.egg-info/SOURCES.txt x pysam-0.7.7/pysam.egg-info/._top_level.txt x pysam-0.7.7/pysam.egg-info/top_level.txt x pysam-0.7.7/pysam/.___init__.py x pysam-0.7.7/pysam/__init__.py x pysam-0.7.7/pysam/._csamtools.c x pysam-0.7.7/pysam/csamtools.c x pysam-0.7.7/pysam/._csamtools.pxd x pysam-0.7.7/pysam/csamtools.pxd x pysam-0.7.7/pysam/._csamtools.pyx x pysam-0.7.7/pysam/csamtools.pyx x pysam-0.7.7/pysam/._ctabix.c x pysam-0.7.7/pysam/ctabix.c x pysam-0.7.7/pysam/._ctabix.pxd x pysam-0.7.7/pysam/ctabix.pxd x pysam-0.7.7/pysam/._ctabix.pyx x pysam-0.7.7/pysam/ctabix.pyx x pysam-0.7.7/pysam/._cvcf.c x pysam-0.7.7/pysam/cvcf.c x pysam-0.7.7/pysam/._cvcf.pxd x pysam-0.7.7/pysam/cvcf.pxd x pysam-0.7.7/pysam/._cvcf.pyx x pysam-0.7.7/pysam/cvcf.pyx x pysam-0.7.7/pysam/include/ x pysam-0.7.7/pysam/._namedtuple.py x pysam-0.7.7/pysam/namedtuple.py x pysam-0.7.7/pysam/._Pileup.py x pysam-0.7.7/pysam/Pileup.py x pysam-0.7.7/pysam/._pysam_util.c x pysam-0.7.7/pysam/pysam_util.c x pysam-0.7.7/pysam/._pysam_util.h x pysam-0.7.7/pysam/pysam_util.h x pysam-0.7.7/pysam/._tabix_util.c x pysam-0.7.7/pysam/tabix_util.c x pysam-0.7.7/pysam/._tabix_util.h x pysam-0.7.7/pysam/tabix_util.h x pysam-0.7.7/pysam/._TabProxies.c x pysam-0.7.7/pysam/TabProxies.c x pysam-0.7.7/pysam/._TabProxies.pxd x pysam-0.7.7/pysam/TabProxies.pxd x pysam-0.7.7/pysam/._TabProxies.pyx x pysam-0.7.7/pysam/TabProxies.pyx x pysam-0.7.7/pysam/._version.py x pysam-0.7.7/pysam/version.py x pysam-0.7.7/pysam/include/.___init__.py x pysam-0.7.7/pysam/include/__init__.py x pysam-0.7.7/doc/._api.rst x pysam-0.7.7/doc/api.rst x pysam-0.7.7/doc/._conf.py x pysam-0.7.7/doc/conf.py x pysam-0.7.7/doc/._contents.rst x pysam-0.7.7/doc/contents.rst x pysam-0.7.7/doc/._developer.rst x pysam-0.7.7/doc/developer.rst x pysam-0.7.7/doc/._faq.rst x pysam-0.7.7/doc/faq.rst x pysam-0.7.7/doc/._glossary.rst x pysam-0.7.7/doc/glossary.rst x pysam-0.7.7/doc/._make.bat x pysam-0.7.7/doc/make.bat x pysam-0.7.7/doc/._Makefile x pysam-0.7.7/doc/Makefile x pysam-0.7.7/doc/._release.rst x pysam-0.7.7/doc/release.rst x pysam-0.7.7/doc/._usage.rst x pysam-0.7.7/doc/usage.rst /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'use_2to3' warnings.warn(msg) running build running build_py creating build creating build/lib.macosx-10.6-intel-2.7 creating build/lib.macosx-10.6-intel-2.7/pysam copying pysam/__init__.py -> build/lib.macosx-10.6-intel-2.7/pysam copying pysam/namedtuple.py -> build/lib.macosx-10.6-intel-2.7/pysam copying pysam/Pileup.py -> build/lib.macosx-10.6-intel-2.7/pysam copying pysam/version.py -> build/lib.macosx-10.6-intel-2.7/pysam creating build/lib.macosx-10.6-intel-2.7/pysam/include copying pysam/include/__init__.py -> build/lib.macosx-10.6-intel-2.7/pysam/include creating build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/__init__.py -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools creating build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/bcftools copying samtools/bcftools/__init__.py -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/bcftools creating build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/win32 copying samtools/win32/__init__.py -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/win32 creating build/lib.macosx-10.6-intel-2.7/pysam/include/tabix copying tabix/__init__.py -> build/lib.macosx-10.6-intel-2.7/pysam/include/tabix copying pysam/csamtools.pxd -> build/lib.macosx-10.6-intel-2.7/pysam copying pysam/ctabix.pxd -> build/lib.macosx-10.6-intel-2.7/pysam copying pysam/cvcf.pxd -> build/lib.macosx-10.6-intel-2.7/pysam copying pysam/TabProxies.pxd -> build/lib.macosx-10.6-intel-2.7/pysam copying pysam/pysam_util.h -> build/lib.macosx-10.6-intel-2.7/pysam copying pysam/tabix_util.h -> build/lib.macosx-10.6-intel-2.7/pysam copying samtools/bam.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/bam2bcf.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/bam_endian.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/bam_tview.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/bgzf.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/errmod.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/faidx.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/kaln.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/khash.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/klist.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/knetfile.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/kprobaln.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/kseq.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/ksort.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/kstring.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/pysam.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/razf.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/sam.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/sam_header.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/sample.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools copying samtools/bcftools/bcf.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/bcftools copying samtools/bcftools/kmin.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/bcftools copying samtools/bcftools/prob1.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/bcftools copying samtools/win32/xcurses.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/win32 copying samtools/win32/zconf.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/win32 copying samtools/win32/zlib.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/win32 copying tabix/bam_endian.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/tabix copying tabix/bgzf.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/tabix copying tabix/khash.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/tabix copying tabix/knetfile.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/tabix copying tabix/kseq.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/tabix copying tabix/ksort.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/tabix copying tabix/kstring.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/tabix copying tabix/pysam.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/tabix copying tabix/tabix.h -> build/lib.macosx-10.6-intel-2.7/pysam/include/tabix running build_ext building 'pysam.csamtools' extension creating build/temp.macosx-10.6-intel-2.7 creating build/temp.macosx-10.6-intel-2.7/pysam creating build/temp.macosx-10.6-intel-2.7/samtools creating build/temp.macosx-10.6-intel-2.7/samtools/bcftools creating build/temp.macosx-10.6-intel-2.7/samtools/misc /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/csamtools.c -o build/temp.macosx-10.6-intel-2.7/pysam/csamtools.o pysam/csamtools.c:12717:167: warning: incompatible pointer types passing 'int (bam1_t *, void *)' to parameter of type 'bam_fetch_f' (aka 'int (*)(const bam1_t *, void *)') [-Wincompatible-pointer-types] __pyx_t_5 = PyInt_FromLong(bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)__pyx_v_callback), __pyx_f_5pysam_9csamtools_fetch_callback)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1071; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam.h:644:103: note: passing argument to parameter 'func' here int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func); ^ pysam/csamtools.c:13182:210: warning: incompatible pointer types passing 'int (bam1_t *, void *)' to parameter of type 'bam_fetch_f' (aka 'int (*)(const bam1_t *, void *)') [-Wincompatible-pointer-types] bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_read->_delegate->core.mtid, __pyx_v_read->_delegate->core.mpos, (__pyx_v_read->_delegate->core.mpos + 1), ((void *)(&__pyx_v_mate_data)), __pyx_f_5pysam_9csamtools_mate_callback); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam.h:644:103: note: passing argument to parameter 'func' here int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func); ^ pysam/csamtools.c:13680:140: warning: incompatible pointer types passing 'int (bam1_t *, void *)' to parameter of type 'bam_fetch_f' (aka 'int (*)(const bam1_t *, void *)') [-Wincompatible-pointer-types] bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)(&__pyx_v_counter)), __pyx_f_5pysam_9csamtools_count_callback); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam.h:644:103: note: passing argument to parameter 'func' here int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func); ^ pysam/csamtools.c:14120:125: warning: incompatible pointer types passing 'int (bam1_t *, void *)' to parameter of type 'bam_fetch_f' (aka 'int (*)(const bam1_t *, void *)') [-Wincompatible-pointer-types] bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, __pyx_v_buf, __pyx_f_5pysam_9csamtools_pileup_fetch_callback); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam.h:644:103: note: passing argument to parameter 'func' here int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func); ^ pysam/csamtools.c:20819:7: warning: implicit declaration of function 'bam_prob_realn' is invalid in C99 [-Wimplicit-function-declaration] bam_prob_realn(__pyx_v_b, __pyx_v_d->seq); ^ pysam/csamtools.c:20847:19: warning: implicit declaration of function 'bam_cap_mapQ' is invalid in C99 [-Wimplicit-function-declaration] __pyx_v_q = bam_cap_mapQ(__pyx_v_b, __pyx_v_d->seq, __pyx_v_capQ_thres); ^ pysam/csamtools.c:22394:59: warning: passing 'const bam_pileup1_t **' to parameter of type 'bam_pileup1_t **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] __pyx_t_2 = __pyx_f_5pysam_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/csamtools.c:3832:76: note: passing argument to parameter '__pyx_v_plp' here static PyObject *__pyx_f_5pysam_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp, int __pyx_v_tid, int __pyx_v_pos, int __pyx_v_n) { ^ pysam/csamtools.c:22647:61: warning: passing 'const bam_pileup1_t **' to parameter of type 'bam_pileup1_t **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] __pyx_t_2 = __pyx_f_5pysam_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/csamtools.c:3832:76: note: passing argument to parameter '__pyx_v_plp' here static PyObject *__pyx_f_5pysam_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp, int __pyx_v_tid, int __pyx_v_pos, int __pyx_v_n) { ^ pysam/csamtools.c:48724:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ pysam/csamtools.c:1078:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ pysam/csamtools.c:46971:28: warning: unused function '__Pyx_CyFunction_InitDefaults' [-Wunused-function] static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { ^ pysam/csamtools.c:47471:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ pysam/csamtools.c:47490:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ pysam/csamtools.c:47585:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ 14 warnings generated. pysam/csamtools.c:12717:167: warning: incompatible pointer types passing 'int (bam1_t *, void *)' to parameter of type 'bam_fetch_f' (aka 'int (*)(const bam1_t *, void *)') [-Wincompatible-pointer-types] __pyx_t_5 = PyInt_FromLong(bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)__pyx_v_callback), __pyx_f_5pysam_9csamtools_fetch_callback)); if (unlikely(!__pyx_t_5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1071; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam.h:644:103: note: passing argument to parameter 'func' here int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func); ^ pysam/csamtools.c:13182:210: warning: incompatible pointer types passing 'int (bam1_t *, void *)' to parameter of type 'bam_fetch_f' (aka 'int (*)(const bam1_t *, void *)') [-Wincompatible-pointer-types] bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_read->_delegate->core.mtid, __pyx_v_read->_delegate->core.mpos, (__pyx_v_read->_delegate->core.mpos + 1), ((void *)(&__pyx_v_mate_data)), __pyx_f_5pysam_9csamtools_mate_callback); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam.h:644:103: note: passing argument to parameter 'func' here int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func); ^ pysam/csamtools.c:13680:140: warning: incompatible pointer types passing 'int (bam1_t *, void *)' to parameter of type 'bam_fetch_f' (aka 'int (*)(const bam1_t *, void *)') [-Wincompatible-pointer-types] bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, ((void *)(&__pyx_v_counter)), __pyx_f_5pysam_9csamtools_count_callback); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam.h:644:103: note: passing argument to parameter 'func' here int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func); ^ pysam/csamtools.c:14120:125: warning: incompatible pointer types passing 'int (bam1_t *, void *)' to parameter of type 'bam_fetch_f' (aka 'int (*)(const bam1_t *, void *)') [-Wincompatible-pointer-types] bam_fetch(__pyx_v_self->samfile->x.bam, __pyx_v_self->index, __pyx_v_rtid, __pyx_v_rstart, __pyx_v_rend, __pyx_v_buf, __pyx_f_5pysam_9csamtools_pileup_fetch_callback); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ samtools/bam.h:644:103: note: passing argument to parameter 'func' here int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func); ^ pysam/csamtools.c:20819:7: warning: implicit declaration of function 'bam_prob_realn' is invalid in C99 [-Wimplicit-function-declaration] bam_prob_realn(__pyx_v_b, __pyx_v_d->seq); ^ pysam/csamtools.c:20847:19: warning: implicit declaration of function 'bam_cap_mapQ' is invalid in C99 [-Wimplicit-function-declaration] __pyx_v_q = bam_cap_mapQ(__pyx_v_b, __pyx_v_d->seq, __pyx_v_capQ_thres); ^ pysam/csamtools.c:22394:59: warning: passing 'const bam_pileup1_t **' to parameter of type 'bam_pileup1_t **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] __pyx_t_2 = __pyx_f_5pysam_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2118; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/csamtools.c:3832:76: note: passing argument to parameter '__pyx_v_plp' here static PyObject *__pyx_f_5pysam_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp, int __pyx_v_tid, int __pyx_v_pos, int __pyx_v_n) { ^ pysam/csamtools.c:22647:61: warning: passing 'const bam_pileup1_t **' to parameter of type 'bam_pileup1_t **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] __pyx_t_2 = __pyx_f_5pysam_9csamtools_makePileupProxy((&__pyx_v_self->__pyx_base.plp), __pyx_v_self->__pyx_base.tid, __pyx_v_self->__pyx_base.pos, __pyx_v_self->__pyx_base.n_plp); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 2149; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/csamtools.c:3832:76: note: passing argument to parameter '__pyx_v_plp' here static PyObject *__pyx_f_5pysam_9csamtools_makePileupProxy(bam_pileup1_t **__pyx_v_plp, int __pyx_v_tid, int __pyx_v_pos, int __pyx_v_n) { ^ pysam/csamtools.c:48724:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ pysam/csamtools.c:1078:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ pysam/csamtools.c:46971:28: warning: unused function '__Pyx_CyFunction_InitDefaults' [-Wunused-function] static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { ^ pysam/csamtools.c:47471:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ pysam/csamtools.c:47490:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ pysam/csamtools.c:47585:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ 14 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/pysam_util.c -o build/temp.macosx-10.6-intel-2.7/pysam/pysam_util.o pysam/pysam_util.c:196:8: warning: assigning to 'bam_pileup1_t *' from 'const bam_pileup1_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] *plp = bam_plp_next(buf->iter, tid, pos, n_plp); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/pysam_util.c:422:18: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if (offset < 0 || offset > b->data_len) ~~~~~~ ^ ~ In file included from pysam/pysam_util.c:8: pysam/pysam_util.h:8:1: warning: unused function 'kseq_init' [-Wunused-function] KSEQ_INIT(gzFile, gzread) ^ samtools/kseq.h:226:35: note: expanded from macro 'KSEQ_INIT' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ samtools/kseq.h:223:2: note: expanded from macro 'KSEQ_INIT2' __KSEQ_BASIC(SCOPE, type_t) \ ^ samtools/kseq.h:152:16: note: expanded from macro '__KSEQ_BASIC' SCOPE kseq_t *kseq_init(type_t fd) \ ^ In file included from pysam/pysam_util.c:8: pysam/pysam_util.h:8:1: warning: unused function 'kseq_destroy' [-Wunused-function] samtools/kseq.h:226:35: note: expanded from macro 'KSEQ_INIT' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ samtools/kseq.h:223:2: note: expanded from macro 'KSEQ_INIT2' __KSEQ_BASIC(SCOPE, type_t) \ ^ samtools/kseq.h:158:13: note: expanded from macro '__KSEQ_BASIC' SCOPE void kseq_destroy(kseq_t *ks) \ ^ In file included from pysam/pysam_util.c:8: pysam/pysam_util.h:8:1: warning: unused function 'kseq_read' [-Wunused-function] samtools/kseq.h:226:35: note: expanded from macro 'KSEQ_INIT' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ samtools/kseq.h:224:2: note: expanded from macro 'KSEQ_INIT2' __KSEQ_READ(SCOPE) ^ samtools/kseq.h:172:12: note: expanded from macro '__KSEQ_READ' SCOPE int kseq_read(kseq_t *seq) \ ^ pysam/pysam_util.c:66:1: warning: unused function 'kh_init_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, bam_binlist_t); ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :260:1: note: expanded from here kh_init_i ^ pysam/pysam_util.c:66:1: warning: unused function 'kh_destroy_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :265:1: note: expanded from here kh_destroy_i ^ pysam/pysam_util.c:66:1: warning: unused function 'kh_clear_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :268:1: note: expanded from here kh_clear_i ^ pysam/pysam_util.c:66:1: warning: unused function 'kh_put_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :9:1: note: expanded from here kh_put_i ^ pysam/pysam_util.c:66:1: warning: unused function 'kh_del_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :14:1: note: expanded from here kh_del_i ^ pysam/pysam_util.c:67:1: warning: unused function 'kh_init_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :21:1: note: expanded from here kh_init_s ^ pysam/pysam_util.c:67:1: warning: unused function 'kh_destroy_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :26:1: note: expanded from here kh_destroy_s ^ pysam/pysam_util.c:67:1: warning: unused function 'kh_clear_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :29:1: note: expanded from here kh_clear_s ^ pysam/pysam_util.c:67:1: warning: unused function 'kh_put_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :38:1: note: expanded from here kh_put_s ^ pysam/pysam_util.c:67:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :43:1: note: expanded from here kh_del_s ^ pysam/pysam_util.c:99:19: warning: unused function 'mp_init' [-Wunused-function] static mempool_t *mp_init() ^ pysam/pysam_util.c:105:13: warning: unused function 'mp_destroy' [-Wunused-function] static void mp_destroy(mempool_t *mp) ^ pysam/pysam_util.c:115:25: warning: unused function 'mp_alloc' [-Wunused-function] static inline lbnode_t *mp_alloc(mempool_t *mp) ^ pysam/pysam_util.c:121:20: warning: unused function 'mp_free' [-Wunused-function] static inline void mp_free(mempool_t *mp, lbnode_t *p) ^ pysam/pysam_util.c:131:19: warning: unused function 'resolve_cigar' [-Wunused-function] static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos) ^ 20 warnings generated. pysam/pysam_util.c:196:8: warning: assigning to 'bam_pileup1_t *' from 'const bam_pileup1_t *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] *plp = bam_plp_next(buf->iter, tid, pos, n_plp); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/pysam_util.c:422:18: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if (offset < 0 || offset > b->data_len) ~~~~~~ ^ ~ In file included from pysam/pysam_util.c:8: pysam/pysam_util.h:8:1: warning: unused function 'kseq_init' [-Wunused-function] KSEQ_INIT(gzFile, gzread) ^ samtools/kseq.h:226:35: note: expanded from macro 'KSEQ_INIT' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ samtools/kseq.h:223:2: note: expanded from macro 'KSEQ_INIT2' __KSEQ_BASIC(SCOPE, type_t) \ ^ samtools/kseq.h:152:16: note: expanded from macro '__KSEQ_BASIC' SCOPE kseq_t *kseq_init(type_t fd) \ ^ In file included from pysam/pysam_util.c:8: pysam/pysam_util.h:8:1: warning: unused function 'kseq_destroy' [-Wunused-function] samtools/kseq.h:226:35: note: expanded from macro 'KSEQ_INIT' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ samtools/kseq.h:223:2: note: expanded from macro 'KSEQ_INIT2' __KSEQ_BASIC(SCOPE, type_t) \ ^ samtools/kseq.h:158:13: note: expanded from macro '__KSEQ_BASIC' SCOPE void kseq_destroy(kseq_t *ks) \ ^ In file included from pysam/pysam_util.c:8: pysam/pysam_util.h:8:1: warning: unused function 'kseq_read' [-Wunused-function] samtools/kseq.h:226:35: note: expanded from macro 'KSEQ_INIT' #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) ^ samtools/kseq.h:224:2: note: expanded from macro 'KSEQ_INIT2' __KSEQ_READ(SCOPE) ^ samtools/kseq.h:172:12: note: expanded from macro '__KSEQ_READ' SCOPE int kseq_read(kseq_t *seq) \ ^ pysam/pysam_util.c:66:1: warning: unused function 'kh_init_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, bam_binlist_t); ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :260:1: note: expanded from here kh_init_i ^ pysam/pysam_util.c:66:1: warning: unused function 'kh_destroy_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :265:1: note: expanded from here kh_destroy_i ^ pysam/pysam_util.c:66:1: warning: unused function 'kh_clear_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :268:1: note: expanded from here kh_clear_i ^ pysam/pysam_util.c:66:1: warning: unused function 'kh_put_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :9:1: note: expanded from here kh_put_i ^ pysam/pysam_util.c:66:1: warning: unused function 'kh_del_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :14:1: note: expanded from here kh_del_i ^ pysam/pysam_util.c:67:1: warning: unused function 'kh_init_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :21:1: note: expanded from here kh_init_s ^ pysam/pysam_util.c:67:1: warning: unused function 'kh_destroy_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :26:1: note: expanded from here kh_destroy_s ^ pysam/pysam_util.c:67:1: warning: unused function 'kh_clear_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :29:1: note: expanded from here kh_clear_s ^ pysam/pysam_util.c:67:1: warning: unused function 'kh_put_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :38:1: note: expanded from here kh_put_s ^ pysam/pysam_util.c:67:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :43:1: note: expanded from here kh_del_s ^ pysam/pysam_util.c:99:19: warning: unused function 'mp_init' [-Wunused-function] static mempool_t *mp_init() ^ pysam/pysam_util.c:105:13: warning: unused function 'mp_destroy' [-Wunused-function] static void mp_destroy(mempool_t *mp) ^ pysam/pysam_util.c:115:25: warning: unused function 'mp_alloc' [-Wunused-function] static inline lbnode_t *mp_alloc(mempool_t *mp) ^ pysam/pysam_util.c:121:20: warning: unused function 'mp_free' [-Wunused-function] static inline void mp_free(mempool_t *mp, lbnode_t *p) ^ pysam/pysam_util.c:131:19: warning: unused function 'resolve_cigar' [-Wunused-function] static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos) ^ 20 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam2bcf.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam2bcf.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam2bcf_indel.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam2bcf_indel.c.pysam.o samtools/bam2bcf_indel.c.pysam.c:34:52: warning: for loop has empty body [-Wempty-body] for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p; ^ samtools/bam2bcf_indel.c.pysam.c:34:52: note: put the semicolon on a separate line to silence this warning samtools/bam2bcf_indel.c.pysam.c:35:52: warning: for loop has empty body [-Wempty-body] for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q; ^ samtools/bam2bcf_indel.c.pysam.c:35:52: note: put the semicolon on a separate line to silence this warning samtools/bam2bcf_indel.c.pysam.c:11:1: warning: unused function 'kh_clear_rg' [-Wunused-function] KHASH_SET_INIT_STR(rg) ^ samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :248:1: note: expanded from here kh_clear_rg ^ samtools/bam2bcf_indel.c.pysam.c:11:1: warning: unused function 'kh_del_rg' [-Wunused-function] samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :262:1: note: expanded from here kh_del_rg ^ 4 warnings generated. samtools/bam2bcf_indel.c.pysam.c:34:52: warning: for loop has empty body [-Wempty-body] for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p; ^ samtools/bam2bcf_indel.c.pysam.c:34:52: note: put the semicolon on a separate line to silence this warning samtools/bam2bcf_indel.c.pysam.c:35:52: warning: for loop has empty body [-Wempty-body] for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q; ^ samtools/bam2bcf_indel.c.pysam.c:35:52: note: put the semicolon on a separate line to silence this warning samtools/bam2bcf_indel.c.pysam.c:11:1: warning: unused function 'kh_clear_rg' [-Wunused-function] KHASH_SET_INIT_STR(rg) ^ samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :248:1: note: expanded from here kh_clear_rg ^ samtools/bam2bcf_indel.c.pysam.c:11:1: warning: unused function 'kh_del_rg' [-Wunused-function] samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :262:1: note: expanded from here kh_del_rg ^ 4 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam2depth.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam2depth.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_aux.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_aux.c.pysam.o samtools/bam_aux.c.pysam.c:7:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :248:1: note: expanded from here kh_clear_s ^ samtools/bam_aux.c.pysam.c:7:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :262:1: note: expanded from here kh_del_s ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_init_r2l' [-Wunused-function] KHASH_MAP_INIT_STR(r2l, str_p) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :269:1: note: expanded from here kh_init_r2l ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :274:1: note: expanded from here kh_destroy_r2l ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_clear_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :277:1: note: expanded from here kh_clear_r2l ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_get_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :280:1: note: expanded from here kh_get_r2l ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_put_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :286:1: note: expanded from here kh_put_r2l ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_del_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :3:1: note: expanded from here kh_del_r2l ^ 8 warnings generated. samtools/bam_aux.c.pysam.c:7:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :248:1: note: expanded from here kh_clear_s ^ samtools/bam_aux.c.pysam.c:7:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :262:1: note: expanded from here kh_del_s ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_init_r2l' [-Wunused-function] KHASH_MAP_INIT_STR(r2l, str_p) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:168:23: note: expanded from macro 'KHASH_INIT2' SCOPE kh_##name##_t *kh_init_##name() { \ ^ :269:1: note: expanded from here kh_init_r2l ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_destroy_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:171:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_destroy_##name(kh_##name##_t *h) \ ^ :274:1: note: expanded from here kh_destroy_r2l ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_clear_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :277:1: note: expanded from here kh_clear_r2l ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_get_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :280:1: note: expanded from here kh_get_r2l ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_put_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:260:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_put_##name(kh_##name##_t *h, khkey_t key, int *ret) \ ^ :286:1: note: expanded from here kh_put_r2l ^ samtools/bam_aux.c.pysam.c:8:1: warning: unused function 'kh_del_r2l' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :3:1: note: expanded from here kh_del_r2l ^ 8 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_cat.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_cat.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_color.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_color.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_import.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_import.c.pysam.o samtools/bam_import.c.pysam.c:20:1: warning: unused function 'kh_clear_ref' [-Wunused-function] KHASH_MAP_INIT_STR(ref, uint64_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :248:1: note: expanded from here kh_clear_ref ^ samtools/bam_import.c.pysam.c:20:1: warning: unused function 'kh_get_ref' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :251:1: note: expanded from here kh_get_ref ^ samtools/bam_import.c.pysam.c:20:1: warning: unused function 'kh_del_ref' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :262:1: note: expanded from here kh_del_ref ^ 3 warnings generated. samtools/bam_import.c.pysam.c:20:1: warning: unused function 'kh_clear_ref' [-Wunused-function] KHASH_MAP_INIT_STR(ref, uint64_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :248:1: note: expanded from here kh_clear_ref ^ samtools/bam_import.c.pysam.c:20:1: warning: unused function 'kh_get_ref' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :251:1: note: expanded from here kh_get_ref ^ samtools/bam_import.c.pysam.c:20:1: warning: unused function 'kh_del_ref' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :262:1: note: expanded from here kh_del_ref ^ 3 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_index.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_index.c.pysam.o samtools/bam_index.c.pysam.c:66:1: warning: unused function 'kh_clear_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, bam_binlist_t) ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :268:1: note: expanded from here kh_clear_i ^ samtools/bam_index.c.pysam.c:66:1: warning: unused function 'kh_del_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :10:1: note: expanded from here kh_del_i ^ 2 warnings generated. samtools/bam_index.c.pysam.c:66:1: warning: unused function 'kh_clear_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, bam_binlist_t) ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :268:1: note: expanded from here kh_clear_i ^ samtools/bam_index.c.pysam.c:66:1: warning: unused function 'kh_del_i' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :10:1: note: expanded from here kh_del_i ^ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_lpileup.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_lpileup.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_mate.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_mate.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_md.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_md.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_pileup.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_pileup.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_plcmd.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_plcmd.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_reheader.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_reheader.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_rmdup.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_rmdup.c.pysam.o samtools/bam_rmdup.c.pysam.c:14:1: warning: unused function 'kh_get_pos' [-Wunused-function] KHASH_MAP_INIT_INT64(pos, bam1_p) ^ samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :280:1: note: expanded from here kh_get_pos ^ samtools/bam_rmdup.c.pysam.c:14:1: warning: unused function 'kh_del_pos' [-Wunused-function] samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :11:1: note: expanded from here kh_del_pos ^ samtools/bam_rmdup.c.pysam.c:22:1: warning: unused function 'kh_clear_lib' [-Wunused-function] KHASH_MAP_INIT_STR(lib, lib_aux_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :28:1: note: expanded from here kh_clear_lib ^ samtools/bam_rmdup.c.pysam.c:22:1: warning: unused function 'kh_del_lib' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :42:1: note: expanded from here kh_del_lib ^ 4 warnings generated. samtools/bam_rmdup.c.pysam.c:14:1: warning: unused function 'kh_get_pos' [-Wunused-function] KHASH_MAP_INIT_INT64(pos, bam1_p) ^ samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :280:1: note: expanded from here kh_get_pos ^ samtools/bam_rmdup.c.pysam.c:14:1: warning: unused function 'kh_del_pos' [-Wunused-function] samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :11:1: note: expanded from here kh_del_pos ^ samtools/bam_rmdup.c.pysam.c:22:1: warning: unused function 'kh_clear_lib' [-Wunused-function] KHASH_MAP_INIT_STR(lib, lib_aux_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :28:1: note: expanded from here kh_clear_lib ^ samtools/bam_rmdup.c.pysam.c:22:1: warning: unused function 'kh_del_lib' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :42:1: note: expanded from here kh_del_lib ^ 4 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_rmdupse.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_rmdupse.c.pysam.o samtools/bam_rmdupse.c.pysam.c:20:1: warning: unused function 'kh_clear_best' [-Wunused-function] KHASH_MAP_INIT_INT(best, elem_p) ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :135:1: note: expanded from here kh_clear_best ^ samtools/bam_rmdupse.c.pysam.c:20:1: warning: unused function 'kh_get_best' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :138:1: note: expanded from here kh_get_best ^ samtools/bam_rmdupse.c.pysam.c:27:1: warning: unused function 'kh_clear_lib' [-Wunused-function] KHASH_MAP_INIT_STR(lib, lib_aux_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :166:1: note: expanded from here kh_clear_lib ^ samtools/bam_rmdupse.c.pysam.c:27:1: warning: unused function 'kh_del_lib' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :180:1: note: expanded from here kh_del_lib ^ 4 warnings generated. samtools/bam_rmdupse.c.pysam.c:20:1: warning: unused function 'kh_clear_best' [-Wunused-function] KHASH_MAP_INIT_INT(best, elem_p) ^ samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :135:1: note: expanded from here kh_clear_best ^ samtools/bam_rmdupse.c.pysam.c:20:1: warning: unused function 'kh_get_best' [-Wunused-function] samtools/khash.h:495:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, khint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:186:16: note: expanded from macro 'KHASH_INIT2' SCOPE khint_t kh_get_##name(const kh_##name##_t *h, khkey_t key) \ ^ :138:1: note: expanded from here kh_get_best ^ samtools/bam_rmdupse.c.pysam.c:27:1: warning: unused function 'kh_clear_lib' [-Wunused-function] KHASH_MAP_INIT_STR(lib, lib_aux_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :166:1: note: expanded from here kh_clear_lib ^ samtools/bam_rmdupse.c.pysam.c:27:1: warning: unused function 'kh_del_lib' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :180:1: note: expanded from here kh_del_lib ^ 4 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_sort.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_sort.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_stat.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_stat.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_tview.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_tview.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_tview_curses.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_tview_curses.c.pysam.o samtools/bam_tview_curses.c.pysam.c:289:2: warning: "No curses library is available; tview with curses is disabled." [-W#warnings] #warning "No curses library is available; tview with curses is disabled." ^ 1 warning generated. samtools/bam_tview_curses.c.pysam.c:289:2: warning: "No curses library is available; tview with curses is disabled." [-W#warnings] #warning "No curses library is available; tview with curses is disabled." ^ 1 warning generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bam_tview_html.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bam_tview_html.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bamshuf.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bamshuf.c.pysam.o samtools/bamshuf.c.pysam.c:107:8: warning: unused variable '_l' [-Wunused-variable] int _l = bam_read1(fp, a[j].b); ^ 1 warning generated. samtools/bamshuf.c.pysam.c:107:8: warning: unused variable '_l' [-Wunused-variable] int _l = bam_read1(fp, a[j].b); ^ 1 warning generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bedcov.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bedcov.c.pysam.o samtools/bedcov.c.pysam.c:14:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 16384) ^ samtools/kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ samtools/kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. samtools/bedcov.c.pysam.c:14:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 16384) ^ samtools/kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ samtools/kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bedidx.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bedidx.c.pysam.o samtools/bedidx.c.pysam.c:26:1: warning: unused function 'kh_clear_reg' [-Wunused-function] KHASH_MAP_INIT_STR(reg, bed_reglist_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :262:1: note: expanded from here kh_clear_reg ^ samtools/bedidx.c.pysam.c:26:1: warning: unused function 'kh_del_reg' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :10:1: note: expanded from here kh_del_reg ^ 2 warnings generated. samtools/bedidx.c.pysam.c:26:1: warning: unused function 'kh_clear_reg' [-Wunused-function] KHASH_MAP_INIT_STR(reg, bed_reglist_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :262:1: note: expanded from here kh_clear_reg ^ samtools/bedidx.c.pysam.c:26:1: warning: unused function 'kh_del_reg' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :10:1: note: expanded from here kh_del_reg ^ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bgzf.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bgzf.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/cut_target.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/cut_target.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/errmod.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/errmod.c.pysam.o samtools/errmod.c.pysam.c:81:8: warning: self-comparison always evaluates to false [-Wtautological-compare] if (m > m) return -1; ^ 1 warning generated. samtools/errmod.c.pysam.c:81:8: warning: self-comparison always evaluates to false [-Wtautological-compare] if (m > m) return -1; ^ 1 warning generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/faidx.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/faidx.c.pysam.o samtools/faidx.c.pysam.c:16:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, faidx1_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :194:1: note: expanded from here kh_clear_s ^ samtools/faidx.c.pysam.c:16:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :208:1: note: expanded from here kh_del_s ^ 2 warnings generated. samtools/faidx.c.pysam.c:16:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, faidx1_t) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :194:1: note: expanded from here kh_clear_s ^ samtools/faidx.c.pysam.c:16:1: warning: unused function 'kh_del_s' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :208:1: note: expanded from here kh_del_s ^ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/kaln.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/kaln.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/knetfile.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/knetfile.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/kprobaln.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/kprobaln.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/kstring.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/kstring.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/padding.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/padding.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/phase.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/phase.c.pysam.o samtools/phase.c.pysam.c:47:1: warning: unused function 'kh_clear_set64' [-Wunused-function] KHASH_SET_INIT_INT64(set64) ^ samtools/khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64' KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :61:1: note: expanded from here kh_clear_set64 ^ samtools/phase.c.pysam.c:47:1: warning: unused function 'kh_del_set64' [-Wunused-function] samtools/khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64' KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :75:1: note: expanded from here kh_del_set64 ^ samtools/phase.c.pysam.c:48:1: warning: unused function 'kh_clear_64' [-Wunused-function] KHASH_MAP_INIT_INT64(64, frag_t) ^ samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :90:1: note: expanded from here kh_clear_64 ^ 3 warnings generated. samtools/phase.c.pysam.c:47:1: warning: unused function 'kh_clear_set64' [-Wunused-function] KHASH_SET_INIT_INT64(set64) ^ samtools/khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64' KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :61:1: note: expanded from here kh_clear_set64 ^ samtools/phase.c.pysam.c:47:1: warning: unused function 'kh_del_set64' [-Wunused-function] samtools/khash.h:502:2: note: expanded from macro 'KHASH_SET_INIT_INT64' KHASH_INIT(name, khint64_t, char, 0, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :75:1: note: expanded from here kh_del_set64 ^ samtools/phase.c.pysam.c:48:1: warning: unused function 'kh_clear_64' [-Wunused-function] KHASH_MAP_INIT_INT64(64, frag_t) ^ samtools/khash.h:510:2: note: expanded from macro 'KHASH_MAP_INIT_INT64' KHASH_INIT(name, khint64_t, khval_t, 1, kh_int64_hash_func, kh_int64_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :90:1: note: expanded from here kh_clear_64 ^ 3 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/razf.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/razf.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/sam.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/sam.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/sam_header.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/sam_header.c.pysam.o samtools/sam_header.c.pysam.c:11:1: warning: unused function 'kh_clear_str' [-Wunused-function] KHASH_MAP_INIT_STR(str, const char *) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :194:1: note: expanded from here kh_clear_str ^ samtools/sam_header.c.pysam.c:11:1: warning: unused function 'kh_del_str' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :208:1: note: expanded from here kh_del_str ^ 2 warnings generated. samtools/sam_header.c.pysam.c:11:1: warning: unused function 'kh_clear_str' [-Wunused-function] KHASH_MAP_INIT_STR(str, const char *) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :194:1: note: expanded from here kh_clear_str ^ samtools/sam_header.c.pysam.c:11:1: warning: unused function 'kh_del_str' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :208:1: note: expanded from here kh_del_str ^ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/sam_view.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/sam_view.c.pysam.o samtools/sam_view.c.pysam.c:14:1: warning: unused function 'kh_clear_rg' [-Wunused-function] KHASH_SET_INIT_STR(rg) ^ samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :57:1: note: expanded from here kh_clear_rg ^ samtools/sam_view.c.pysam.c:14:1: warning: unused function 'kh_del_rg' [-Wunused-function] samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :71:1: note: expanded from here kh_del_rg ^ 2 warnings generated. samtools/sam_view.c.pysam.c:14:1: warning: unused function 'kh_clear_rg' [-Wunused-function] KHASH_SET_INIT_STR(rg) ^ samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :57:1: note: expanded from here kh_clear_rg ^ samtools/sam_view.c.pysam.c:14:1: warning: unused function 'kh_del_rg' [-Wunused-function] samtools/khash.h:518:2: note: expanded from macro 'KHASH_SET_INIT_STR' KHASH_INIT(name, kh_cstr_t, char, 0, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :71:1: note: expanded from here kh_del_rg ^ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/sample.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/sample.c.pysam.o samtools/sample.c.pysam.c:7:1: warning: unused function 'kh_clear_sm' [-Wunused-function] KHASH_MAP_INIT_STR(sm, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :194:1: note: expanded from here kh_clear_sm ^ samtools/sample.c.pysam.c:7:1: warning: unused function 'kh_del_sm' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :208:1: note: expanded from here kh_del_sm ^ 2 warnings generated. samtools/sample.c.pysam.c:7:1: warning: unused function 'kh_clear_sm' [-Wunused-function] KHASH_MAP_INIT_STR(sm, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :194:1: note: expanded from here kh_clear_sm ^ samtools/sample.c.pysam.c:7:1: warning: unused function 'kh_del_sm' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :208:1: note: expanded from here kh_del_sm ^ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/bcf.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/bcf.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/bcf2qcall.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/bcf2qcall.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/bcfutils.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/bcfutils.c.pysam.o samtools/bcftools/bcfutils.c.pysam.c:9:1: warning: unused function 'kh_clear_str2id' [-Wunused-function] KHASH_MAP_INIT_STR(str2id, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :64:1: note: expanded from here kh_clear_str2id ^ samtools/bcftools/bcfutils.c.pysam.c:9:1: warning: unused function 'kh_del_str2id' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :78:1: note: expanded from here kh_del_str2id ^ 2 warnings generated. samtools/bcftools/bcfutils.c.pysam.c:9:1: warning: unused function 'kh_clear_str2id' [-Wunused-function] KHASH_MAP_INIT_STR(str2id, int) ^ samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:179:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_clear_##name(kh_##name##_t *h) \ ^ :64:1: note: expanded from here kh_clear_str2id ^ samtools/bcftools/bcfutils.c.pysam.c:9:1: warning: unused function 'kh_del_str2id' [-Wunused-function] samtools/khash.h:526:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ samtools/khash.h:307:2: note: expanded from macro 'KHASH_INIT' KHASH_INIT2(name, static inline, khkey_t, khval_t, kh_is_map, __hash_func, __hash_equal) ^ samtools/khash.h:298:13: note: expanded from macro 'KHASH_INIT2' SCOPE void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :78:1: note: expanded from here kh_del_str2id ^ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/call1.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/call1.c.pysam.o samtools/bcftools/call1.c.pysam.c:19:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 16384) ^ samtools/kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ samtools/kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. samtools/bcftools/call1.c.pysam.c:19:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 16384) ^ samtools/kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ samtools/kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/em.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/em.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/fet.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/fet.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/index.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/index.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/kfunc.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/kfunc.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/kmin.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/kmin.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/mut.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/mut.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/prob1.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/prob1.c.pysam.o samtools/bcftools/prob1.c.pysam.c:15:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 16384) ^ samtools/kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ samtools/kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. samtools/bcftools/prob1.c.pysam.c:15:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 16384) ^ samtools/kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ samtools/kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/bcftools/vcf.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/vcf.c.pysam.o samtools/bcftools/vcf.c.pysam.c:245:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] endblock: i = i; ~ ^ ~ samtools/bcftools/vcf.c.pysam.c:10:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 4096) ^ samtools/kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ samtools/kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 2 warnings generated. samtools/bcftools/vcf.c.pysam.c:245:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign] endblock: i = i; ~ ^ ~ samtools/bcftools/vcf.c.pysam.c:10:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 4096) ^ samtools/kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ samtools/kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/misc/ace2sam.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/misc/ace2sam.c.pysam.o samtools/misc/ace2sam.c.pysam.c:35:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 16384) ^ samtools/kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ samtools/kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. samtools/misc/ace2sam.c.pysam.c:35:1: warning: unused function 'ks_getc' [-Wunused-function] KSTREAM_INIT(gzFile, gzread, 16384) ^ samtools/kseq.h:146:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETC(__read, __bufsize) \ ^ samtools/kseq.h:67:20: note: expanded from macro '__KS_GETC' static inline int ks_getc(kstream_t *ks) \ ^ 1 warning generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c samtools/misc/md5.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/samtools/misc/md5.c.pysam.o samtools/misc/md5.c.pysam.c:157:27: warning: 'memset' call operates on objects of type 'struct MD5Context' while the size is based on a different type 'struct MD5Context *' [-Wsizeof-pointer-memaccess] memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ ~~~ ^~~ samtools/misc/md5.c.pysam.c:157:27: note: did you mean to dereference the argument to 'sizeof' (and multiply it by the number of elements)? memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ ^~~ 1 warning generated. samtools/misc/md5.c.pysam.c:157:27: warning: 'memset' call operates on objects of type 'struct MD5Context' while the size is based on a different type 'struct MD5Context *' [-Wsizeof-pointer-memaccess] memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ ~~~ ^~~ samtools/misc/md5.c.pysam.c:157:27: note: did you mean to dereference the argument to 'sizeof' (and multiply it by the number of elements)? memset(ctx, 0, sizeof(ctx)); /* In case it's sensitive */ ^~~ 1 warning generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/pysam/csamtools.o build/temp.macosx-10.6-intel-2.7/pysam/pysam_util.o build/temp.macosx-10.6-intel-2.7/samtools/bam.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam2bcf.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam2bcf_indel.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam2depth.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_aux.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_cat.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_color.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_import.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_index.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_lpileup.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_mate.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_md.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_pileup.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_plcmd.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_reheader.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_rmdup.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_rmdupse.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_sort.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_stat.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_tview.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_tview_curses.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bam_tview_html.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bamshuf.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bedcov.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bedidx.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bgzf.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/cut_target.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/errmod.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/faidx.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/kaln.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/knetfile.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/kprobaln.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/kstring.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/padding.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/phase.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/razf.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/sam.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/sam_header.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/sam_view.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/sample.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/bcf.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/bcf2qcall.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/bcfutils.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/call1.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/em.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/fet.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/index.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/kfunc.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/kmin.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/mut.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/prob1.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/bcftools/vcf.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/misc/ace2sam.c.pysam.o build/temp.macosx-10.6-intel-2.7/samtools/misc/md5.c.pysam.o -lz -o build/lib.macosx-10.6-intel-2.7/pysam/csamtools.so building 'pysam.ctabix' extension creating build/temp.macosx-10.6-intel-2.7/tabix /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/ctabix.c -o build/temp.macosx-10.6-intel-2.7/pysam/ctabix.o pysam/ctabix.c:4151:21: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] __pyx_v_sequences = ti_seqname(__pyx_v_self->tabixfile->idx, (&__pyx_v_nsequences)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/ctabix.c:4652:15: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/ctabix.c:5004:13: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/ctabix.c:5837:15: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/ctabix.c:13711:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ pysam/ctabix.c:13732:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ pysam/ctabix.c:11825:27: warning: unused function '__Pyx_ErrFetch' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { ^ pysam/ctabix.c:832:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { ^ pysam/ctabix.c:852:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ pysam/ctabix.c:12857:28: warning: unused function '__Pyx_CyFunction_InitDefaults' [-Wunused-function] static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { ^ pysam/ctabix.c:12866:27: warning: unused function '__Pyx_CyFunction_SetDefaultsTuple' [-Wunused-function] static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) { ^ pysam/ctabix.c:12986:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ pysam/ctabix.c:13005:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ pysam/ctabix.c:13100:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ pysam/ctabix.c:13224:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ pysam/ctabix.c:1560:18: warning: unused function '__pyx_f_5pysam_6ctabix_from_string_and_size' [-Wunused-function] static PyObject *__pyx_f_5pysam_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) { ^ pysam/ctabix.c:1914:32: warning: unused function '__pyx_f_5pysam_6ctabix__force_cmdline_bytes' [-Wunused-function] static CYTHON_INLINE PyObject *__pyx_f_5pysam_6ctabix__force_cmdline_bytes(PyObject *__pyx_v_s) { ^ pysam/ctabix.c:2030:18: warning: unused function '__pyx_f_5pysam_6ctabix__force_str' [-Wunused-function] static PyObject *__pyx_f_5pysam_6ctabix__force_str(PyObject *__pyx_v_s) { ^ pysam/ctabix.c:7363:18: warning: unused function '__pyx_f_5pysam_6ctabix_buildGzipError' [-Wunused-function] static PyObject *__pyx_f_5pysam_6ctabix_buildGzipError(void *__pyx_v_gzfp) { ^ 19 warnings generated. pysam/ctabix.c:4151:21: warning: assigning to 'char **' from 'const char **' discards qualifiers in nested pointer types [-Wincompatible-pointer-types-discards-qualifiers] __pyx_v_sequences = ti_seqname(__pyx_v_self->tabixfile->idx, (&__pyx_v_nsequences)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/ctabix.c:4652:15: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/ctabix.c:5004:13: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/ctabix.c:5837:15: warning: assigning to 'char *' from 'const char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] __pyx_v_s = ti_read(__pyx_v_self->tabixfile, __pyx_v_self->iterator, (&__pyx_v_len)); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pysam/ctabix.c:13711:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ pysam/ctabix.c:13732:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ pysam/ctabix.c:11825:27: warning: unused function '__Pyx_ErrFetch' [-Wunused-function] static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { ^ pysam/ctabix.c:832:32: warning: unused function '__Pyx_GetItemInt_List_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i) { ^ pysam/ctabix.c:852:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ pysam/ctabix.c:12857:28: warning: unused function '__Pyx_CyFunction_InitDefaults' [-Wunused-function] static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { ^ pysam/ctabix.c:12866:27: warning: unused function '__Pyx_CyFunction_SetDefaultsTuple' [-Wunused-function] static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsTuple(PyObject *func, PyObject *tuple) { ^ pysam/ctabix.c:12986:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ pysam/ctabix.c:13005:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ pysam/ctabix.c:13100:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ pysam/ctabix.c:13224:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ pysam/ctabix.c:1560:18: warning: unused function '__pyx_f_5pysam_6ctabix_from_string_and_size' [-Wunused-function] static PyObject *__pyx_f_5pysam_6ctabix_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) { ^ pysam/ctabix.c:1914:32: warning: unused function '__pyx_f_5pysam_6ctabix__force_cmdline_bytes' [-Wunused-function] static CYTHON_INLINE PyObject *__pyx_f_5pysam_6ctabix__force_cmdline_bytes(PyObject *__pyx_v_s) { ^ pysam/ctabix.c:2030:18: warning: unused function '__pyx_f_5pysam_6ctabix__force_str' [-Wunused-function] static PyObject *__pyx_f_5pysam_6ctabix__force_str(PyObject *__pyx_v_s) { ^ pysam/ctabix.c:7363:18: warning: unused function '__pyx_f_5pysam_6ctabix_buildGzipError' [-Wunused-function] static PyObject *__pyx_f_5pysam_6ctabix_buildGzipError(void *__pyx_v_gzfp) { ^ 19 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/tabix_util.c -o build/temp.macosx-10.6-intel-2.7/pysam/tabix_util.o pysam/tabix_util.c:18:15: warning: implicitly declaring library function 'malloc' with type 'void *(unsigned long)' *line = malloc(*linelen); ^ pysam/tabix_util.c:18:15: note: include the header or explicitly provide a declaration for 'malloc' pysam/tabix_util.c:21:3: warning: implicitly declaring library function 'memset' with type 'void *(void *, int, unsigned long)' memset(*line, 0, *linelen); ^ pysam/tabix_util.c:21:3: note: include the header or explicitly provide a declaration for 'memset' pysam/tabix_util.c:24:11: warning: implicitly declaring library function 'strlen' with type 'unsigned long (const char *)' return (strlen(*line)); ^ pysam/tabix_util.c:24:11: note: include the header or explicitly provide a declaration for 'strlen' 3 warnings generated. pysam/tabix_util.c:18:15: warning: implicitly declaring library function 'malloc' with type 'void *(unsigned long)' *line = malloc(*linelen); ^ pysam/tabix_util.c:18:15: note: include the header or explicitly provide a declaration for 'malloc' pysam/tabix_util.c:21:3: warning: implicitly declaring library function 'memset' with type 'void *(void *, int, unsigned long)' memset(*line, 0, *linelen); ^ pysam/tabix_util.c:21:3: note: include the header or explicitly provide a declaration for 'memset' pysam/tabix_util.c:24:11: warning: implicitly declaring library function 'strlen' with type 'unsigned long (const char *)' return (strlen(*line)); ^ pysam/tabix_util.c:24:11: note: include the header or explicitly provide a declaration for 'strlen' 3 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c tabix/bedidx.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/tabix/bedidx.c.pysam.o tabix/bedidx.c.pysam.c:22:1: warning: unused function 'kh_clear_reg' [-Wunused-function] KHASH_MAP_INIT_STR(reg, bed_reglist_t) ^ tabix/khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ tabix/khash.h:140:21: note: expanded from macro 'KHASH_INIT' static inline void kh_clear_##name(kh_##name##_t *h) \ ^ :260:1: note: expanded from here kh_clear_reg ^ tabix/bedidx.c.pysam.c:22:1: warning: unused function 'kh_del_reg' [-Wunused-function] tabix/khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ tabix/khash.h:259:21: note: expanded from macro 'KHASH_INIT' static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :8:1: note: expanded from here kh_del_reg ^ 2 warnings generated. tabix/bedidx.c.pysam.c:22:1: warning: unused function 'kh_clear_reg' [-Wunused-function] KHASH_MAP_INIT_STR(reg, bed_reglist_t) ^ tabix/khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ tabix/khash.h:140:21: note: expanded from macro 'KHASH_INIT' static inline void kh_clear_##name(kh_##name##_t *h) \ ^ :260:1: note: expanded from here kh_clear_reg ^ tabix/bedidx.c.pysam.c:22:1: warning: unused function 'kh_del_reg' [-Wunused-function] tabix/khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ tabix/khash.h:259:21: note: expanded from macro 'KHASH_INIT' static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :8:1: note: expanded from here kh_del_reg ^ 2 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c tabix/bgzf.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/tabix/bgzf.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c tabix/bgzip.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/tabix/bgzip.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c tabix/index.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/tabix/index.c.pysam.o tabix/index.c.pysam.c:36:1: warning: unused function 'kh_clear_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, ti_binlist_t) ^ tabix/khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ tabix/khash.h:140:21: note: expanded from macro 'KHASH_INIT' static inline void kh_clear_##name(kh_##name##_t *h) \ ^ :60:1: note: expanded from here kh_clear_i ^ tabix/index.c.pysam.c:36:1: warning: unused function 'kh_del_i' [-Wunused-function] tabix/khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ tabix/khash.h:259:21: note: expanded from macro 'KHASH_INIT' static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :74:1: note: expanded from here kh_del_i ^ tabix/index.c.pysam.c:37:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ tabix/khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ tabix/khash.h:140:21: note: expanded from macro 'KHASH_INIT' static inline void kh_clear_##name(kh_##name##_t *h) \ ^ :89:1: note: expanded from here kh_clear_s ^ tabix/index.c.pysam.c:37:1: warning: unused function 'kh_del_s' [-Wunused-function] tabix/khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ tabix/khash.h:259:21: note: expanded from macro 'KHASH_INIT' static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :103:1: note: expanded from here kh_del_s ^ 4 warnings generated. tabix/index.c.pysam.c:36:1: warning: unused function 'kh_clear_i' [-Wunused-function] KHASH_MAP_INIT_INT(i, ti_binlist_t) ^ tabix/khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ tabix/khash.h:140:21: note: expanded from macro 'KHASH_INIT' static inline void kh_clear_##name(kh_##name##_t *h) \ ^ :60:1: note: expanded from here kh_clear_i ^ tabix/index.c.pysam.c:36:1: warning: unused function 'kh_del_i' [-Wunused-function] tabix/khash.h:453:2: note: expanded from macro 'KHASH_MAP_INIT_INT' KHASH_INIT(name, uint32_t, khval_t, 1, kh_int_hash_func, kh_int_hash_equal) ^ tabix/khash.h:259:21: note: expanded from macro 'KHASH_INIT' static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :74:1: note: expanded from here kh_del_i ^ tabix/index.c.pysam.c:37:1: warning: unused function 'kh_clear_s' [-Wunused-function] KHASH_MAP_INIT_STR(s, int) ^ tabix/khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ tabix/khash.h:140:21: note: expanded from macro 'KHASH_INIT' static inline void kh_clear_##name(kh_##name##_t *h) \ ^ :89:1: note: expanded from here kh_clear_s ^ tabix/index.c.pysam.c:37:1: warning: unused function 'kh_del_s' [-Wunused-function] tabix/khash.h:484:2: note: expanded from macro 'KHASH_MAP_INIT_STR' KHASH_INIT(name, kh_cstr_t, khval_t, 1, kh_str_hash_func, kh_str_hash_equal) ^ tabix/khash.h:259:21: note: expanded from macro 'KHASH_INIT' static inline void kh_del_##name(kh_##name##_t *h, khint_t x) \ ^ :103:1: note: expanded from here kh_del_s ^ 4 warnings generated. /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c tabix/knetfile.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/tabix/knetfile.c.pysam.o /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Itabix -Ipysam -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c tabix/kstring.c.pysam.c -o build/temp.macosx-10.6-intel-2.7/tabix/kstring.c.pysam.o /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/pysam/ctabix.o build/temp.macosx-10.6-intel-2.7/pysam/tabix_util.o build/temp.macosx-10.6-intel-2.7/tabix/bedidx.c.pysam.o build/temp.macosx-10.6-intel-2.7/tabix/bgzf.c.pysam.o build/temp.macosx-10.6-intel-2.7/tabix/bgzip.c.pysam.o build/temp.macosx-10.6-intel-2.7/tabix/index.c.pysam.o build/temp.macosx-10.6-intel-2.7/tabix/knetfile.c.pysam.o build/temp.macosx-10.6-intel-2.7/tabix/kstring.c.pysam.o -lz -o build/lib.macosx-10.6-intel-2.7/pysam/ctabix.so building 'pysam.TabProxies' extension /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/TabProxies.c -o build/temp.macosx-10.6-intel-2.7/pysam/TabProxies.o pysam/TabProxies.c:2797:33: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] __pyx_t_4 = (__pyx_v_nbytes < 0); ~~~~~~~~~~~~~~ ^ ~ pysam/TabProxies.c:12655:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ pysam/TabProxies.c:12663:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ pysam/TabProxies.c:12676:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ pysam/TabProxies.c:635:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ pysam/TabProxies.c:11930:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ pysam/TabProxies.c:11949:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ pysam/TabProxies.c:12044:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ pysam/TabProxies.c:12168:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ pysam/TabProxies.c:1180:18: warning: unused function '__pyx_f_5pysam_10TabProxies_from_string_and_size' [-Wunused-function] static PyObject *__pyx_f_5pysam_10TabProxies_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) { ^ pysam/TabProxies.c:1253:18: warning: unused function '__pyx_f_5pysam_10TabProxies__my_encodeFilename' [-Wunused-function] static PyObject *__pyx_f_5pysam_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filename) { ^ pysam/TabProxies.c:1534:32: warning: unused function '__pyx_f_5pysam_10TabProxies__force_cmdline_bytes' [-Wunused-function] static CYTHON_INLINE PyObject *__pyx_f_5pysam_10TabProxies__force_cmdline_bytes(PyObject *__pyx_v_s) { ^ pysam/TabProxies.c:1577:18: warning: unused function '__pyx_f_5pysam_10TabProxies__charptr_to_str' [-Wunused-function] static PyObject *__pyx_f_5pysam_10TabProxies__charptr_to_str(char *__pyx_v_s) { ^ pysam/TabProxies.c:1775:14: warning: unused function '__pyx_f_5pysam_10TabProxies_nextItem' [-Wunused-function] static char *__pyx_f_5pysam_10TabProxies_nextItem(char *__pyx_v_buffer) { ^ 14 warnings generated. pysam/TabProxies.c:2797:33: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] __pyx_t_4 = (__pyx_v_nbytes < 0); ~~~~~~~~~~~~~~ ^ ~ pysam/TabProxies.c:12655:33: warning: unused function '__Pyx_PyIndex_AsSsize_t' [-Wunused-function] static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { ^ pysam/TabProxies.c:12663:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ pysam/TabProxies.c:12676:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ pysam/TabProxies.c:635:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ pysam/TabProxies.c:11930:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ pysam/TabProxies.c:11949:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ pysam/TabProxies.c:12044:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ pysam/TabProxies.c:12168:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ pysam/TabProxies.c:1180:18: warning: unused function '__pyx_f_5pysam_10TabProxies_from_string_and_size' [-Wunused-function] static PyObject *__pyx_f_5pysam_10TabProxies_from_string_and_size(char *__pyx_v_s, size_t __pyx_v_length) { ^ pysam/TabProxies.c:1253:18: warning: unused function '__pyx_f_5pysam_10TabProxies__my_encodeFilename' [-Wunused-function] static PyObject *__pyx_f_5pysam_10TabProxies__my_encodeFilename(PyObject *__pyx_v_filename) { ^ pysam/TabProxies.c:1534:32: warning: unused function '__pyx_f_5pysam_10TabProxies__force_cmdline_bytes' [-Wunused-function] static CYTHON_INLINE PyObject *__pyx_f_5pysam_10TabProxies__force_cmdline_bytes(PyObject *__pyx_v_s) { ^ pysam/TabProxies.c:1577:18: warning: unused function '__pyx_f_5pysam_10TabProxies__charptr_to_str' [-Wunused-function] static PyObject *__pyx_f_5pysam_10TabProxies__charptr_to_str(char *__pyx_v_s) { ^ pysam/TabProxies.c:1775:14: warning: unused function '__pyx_f_5pysam_10TabProxies_nextItem' [-Wunused-function] static char *__pyx_f_5pysam_10TabProxies_nextItem(char *__pyx_v_buffer) { ^ 14 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/pysam/TabProxies.o -lz -o build/lib.macosx-10.6-intel-2.7/pysam/TabProxies.so building 'pysam.cvcf' extension /usr/bin/clang -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Itabix -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c pysam/cvcf.c -o build/temp.macosx-10.6-intel-2.7/pysam/cvcf.o In file included from pysam/cvcf.c:266: pysam/tabix_util.h:12:1: warning: unused function 'ks_getuntil' [-Wunused-function] KSTREAM_INIT( gzFile, gzread, 16384) ^ tabix/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETUNTIL(__read, __bufsize) ^ tabix/kseq.h:97:13: note: expanded from macro '__KS_GETUNTIL' static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \ ^ pysam/cvcf.c:29909:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ pysam/cvcf.c:29922:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ pysam/cvcf.c:970:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ pysam/cvcf.c:28599:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ pysam/cvcf.c:28618:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ pysam/cvcf.c:28637:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ pysam/cvcf.c:28656:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ pysam/cvcf.c:28675:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ pysam/cvcf.c:28713:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ pysam/cvcf.c:28732:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ pysam/cvcf.c:28751:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ pysam/cvcf.c:28770:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ pysam/cvcf.c:28894:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ pysam/cvcf.c:28964:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 15 warnings generated. In file included from pysam/cvcf.c:266: pysam/tabix_util.h:12:1: warning: unused function 'ks_getuntil' [-Wunused-function] KSTREAM_INIT( gzFile, gzread, 16384) ^ tabix/kseq.h:147:2: note: expanded from macro 'KSTREAM_INIT' __KS_GETUNTIL(__read, __bufsize) ^ tabix/kseq.h:97:13: note: expanded from macro '__KS_GETUNTIL' static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \ ^ pysam/cvcf.c:29909:33: warning: unused function '__Pyx_PyInt_FromSize_t' [-Wunused-function] static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) { ^ pysam/cvcf.c:29922:29: warning: unused function '__Pyx_PyInt_AsSize_t' [-Wunused-function] static CYTHON_INLINE size_t __Pyx_PyInt_AsSize_t(PyObject* x) { ^ pysam/cvcf.c:970:32: warning: unused function '__Pyx_GetItemInt_Tuple_Fast' [-Wunused-function] static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i) { ^ pysam/cvcf.c:28599:36: warning: unused function '__Pyx_PyInt_AsUnsignedChar' [-Wunused-function] static CYTHON_INLINE unsigned char __Pyx_PyInt_AsUnsignedChar(PyObject* x) { ^ pysam/cvcf.c:28618:37: warning: unused function '__Pyx_PyInt_AsUnsignedShort' [-Wunused-function] static CYTHON_INLINE unsigned short __Pyx_PyInt_AsUnsignedShort(PyObject* x) { ^ pysam/cvcf.c:28637:35: warning: unused function '__Pyx_PyInt_AsUnsignedInt' [-Wunused-function] static CYTHON_INLINE unsigned int __Pyx_PyInt_AsUnsignedInt(PyObject* x) { ^ pysam/cvcf.c:28656:27: warning: unused function '__Pyx_PyInt_AsChar' [-Wunused-function] static CYTHON_INLINE char __Pyx_PyInt_AsChar(PyObject* x) { ^ pysam/cvcf.c:28675:28: warning: unused function '__Pyx_PyInt_AsShort' [-Wunused-function] static CYTHON_INLINE short __Pyx_PyInt_AsShort(PyObject* x) { ^ pysam/cvcf.c:28713:34: warning: unused function '__Pyx_PyInt_AsSignedChar' [-Wunused-function] static CYTHON_INLINE signed char __Pyx_PyInt_AsSignedChar(PyObject* x) { ^ pysam/cvcf.c:28732:35: warning: unused function '__Pyx_PyInt_AsSignedShort' [-Wunused-function] static CYTHON_INLINE signed short __Pyx_PyInt_AsSignedShort(PyObject* x) { ^ pysam/cvcf.c:28751:33: warning: unused function '__Pyx_PyInt_AsSignedInt' [-Wunused-function] static CYTHON_INLINE signed int __Pyx_PyInt_AsSignedInt(PyObject* x) { ^ pysam/cvcf.c:28770:26: warning: unused function '__Pyx_PyInt_AsLongDouble' [-Wunused-function] static CYTHON_INLINE int __Pyx_PyInt_AsLongDouble(PyObject* x) { ^ pysam/cvcf.c:28894:35: warning: function '__Pyx_PyInt_AsLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE PY_LONG_LONG __Pyx_PyInt_AsLongLong(PyObject* x) { ^ pysam/cvcf.c:28964:42: warning: function '__Pyx_PyInt_AsSignedLongLong' is not needed and will not be emitted [-Wunneeded-internal-declaration] static CYTHON_INLINE signed PY_LONG_LONG __Pyx_PyInt_AsSignedLongLong(PyObject* x) { ^ 15 warnings generated. /usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-2.7/pysam/cvcf.o -lz -o build/lib.macosx-10.6-intel-2.7/pysam/cvcf.so /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'use_2to3' warnings.warn(msg) running install running bdist_egg running egg_info writing requirements to pysam.egg-info/requires.txt writing pysam.egg-info/PKG-INFO writing top-level names to pysam.egg-info/top_level.txt writing dependency_links to pysam.egg-info/dependency_links.txt reading manifest file 'pysam.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'distribute_setup.py' writing manifest file 'pysam.egg-info/SOURCES.txt' installing library code to build/bdist.macosx-10.6-intel/egg running install_lib running build_py running build_ext creating build/bdist.macosx-10.6-intel creating build/bdist.macosx-10.6-intel/egg creating build/bdist.macosx-10.6-intel/egg/pysam copying build/lib.macosx-10.6-intel-2.7/pysam/__init__.py -> build/bdist.macosx-10.6-intel/egg/pysam copying build/lib.macosx-10.6-intel-2.7/pysam/csamtools.pxd -> build/bdist.macosx-10.6-intel/egg/pysam copying build/lib.macosx-10.6-intel-2.7/pysam/csamtools.so -> build/bdist.macosx-10.6-intel/egg/pysam copying build/lib.macosx-10.6-intel-2.7/pysam/ctabix.pxd -> build/bdist.macosx-10.6-intel/egg/pysam copying build/lib.macosx-10.6-intel-2.7/pysam/ctabix.so -> build/bdist.macosx-10.6-intel/egg/pysam copying build/lib.macosx-10.6-intel-2.7/pysam/cvcf.pxd -> build/bdist.macosx-10.6-intel/egg/pysam copying build/lib.macosx-10.6-intel-2.7/pysam/cvcf.so -> build/bdist.macosx-10.6-intel/egg/pysam creating build/bdist.macosx-10.6-intel/egg/pysam/include copying build/lib.macosx-10.6-intel-2.7/pysam/include/__init__.py -> build/bdist.macosx-10.6-intel/egg/pysam/include creating build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/__init__.py -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/bam.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/bam2bcf.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/bam_endian.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/bam_tview.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools creating build/bdist.macosx-10.6-intel/egg/pysam/include/samtools/bcftools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/bcftools/__init__.py -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools/bcftools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/bcftools/bcf.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools/bcftools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/bcftools/kmin.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools/bcftools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/bcftools/prob1.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools/bcftools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/bgzf.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/errmod.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/faidx.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/kaln.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/khash.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/klist.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/knetfile.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/kprobaln.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/kseq.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/ksort.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/kstring.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/pysam.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/razf.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/sam.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/sam_header.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/sample.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools creating build/bdist.macosx-10.6-intel/egg/pysam/include/samtools/win32 copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/win32/__init__.py -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools/win32 copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/win32/xcurses.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools/win32 copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/win32/zconf.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools/win32 copying build/lib.macosx-10.6-intel-2.7/pysam/include/samtools/win32/zlib.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/samtools/win32 creating build/bdist.macosx-10.6-intel/egg/pysam/include/tabix copying build/lib.macosx-10.6-intel-2.7/pysam/include/tabix/__init__.py -> build/bdist.macosx-10.6-intel/egg/pysam/include/tabix copying build/lib.macosx-10.6-intel-2.7/pysam/include/tabix/bam_endian.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/tabix copying build/lib.macosx-10.6-intel-2.7/pysam/include/tabix/bgzf.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/tabix copying build/lib.macosx-10.6-intel-2.7/pysam/include/tabix/khash.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/tabix copying build/lib.macosx-10.6-intel-2.7/pysam/include/tabix/knetfile.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/tabix copying build/lib.macosx-10.6-intel-2.7/pysam/include/tabix/kseq.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/tabix copying build/lib.macosx-10.6-intel-2.7/pysam/include/tabix/ksort.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/tabix copying build/lib.macosx-10.6-intel-2.7/pysam/include/tabix/kstring.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/tabix copying build/lib.macosx-10.6-intel-2.7/pysam/include/tabix/pysam.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/tabix copying build/lib.macosx-10.6-intel-2.7/pysam/include/tabix/tabix.h -> build/bdist.macosx-10.6-intel/egg/pysam/include/tabix copying build/lib.macosx-10.6-intel-2.7/pysam/namedtuple.py -> build/bdist.macosx-10.6-intel/egg/pysam copying build/lib.macosx-10.6-intel-2.7/pysam/Pileup.py -> build/bdist.macosx-10.6-intel/egg/pysam copying build/lib.macosx-10.6-intel-2.7/pysam/pysam_util.h -> build/bdist.macosx-10.6-intel/egg/pysam copying build/lib.macosx-10.6-intel-2.7/pysam/tabix_util.h -> build/bdist.macosx-10.6-intel/egg/pysam copying build/lib.macosx-10.6-intel-2.7/pysam/TabProxies.pxd -> build/bdist.macosx-10.6-intel/egg/pysam copying build/lib.macosx-10.6-intel-2.7/pysam/TabProxies.so -> build/bdist.macosx-10.6-intel/egg/pysam copying build/lib.macosx-10.6-intel-2.7/pysam/version.py -> build/bdist.macosx-10.6-intel/egg/pysam byte-compiling build/bdist.macosx-10.6-intel/egg/pysam/__init__.py to __init__.pyc byte-compiling build/bdist.macosx-10.6-intel/egg/pysam/include/__init__.py to __init__.pyc byte-compiling build/bdist.macosx-10.6-intel/egg/pysam/include/samtools/__init__.py to __init__.pyc byte-compiling build/bdist.macosx-10.6-intel/egg/pysam/include/samtools/bcftools/__init__.py to __init__.pyc byte-compiling build/bdist.macosx-10.6-intel/egg/pysam/include/samtools/win32/__init__.py to __init__.pyc byte-compiling build/bdist.macosx-10.6-intel/egg/pysam/include/tabix/__init__.py to __init__.pyc byte-compiling build/bdist.macosx-10.6-intel/egg/pysam/namedtuple.py to namedtuple.pyc byte-compiling build/bdist.macosx-10.6-intel/egg/pysam/Pileup.py to Pileup.pyc byte-compiling build/bdist.macosx-10.6-intel/egg/pysam/version.py to version.pyc creating stub loader for pysam/csamtools.so creating stub loader for pysam/ctabix.so creating stub loader for pysam/TabProxies.so creating stub loader for pysam/cvcf.so byte-compiling build/bdist.macosx-10.6-intel/egg/pysam/csamtools.py to csamtools.pyc byte-compiling build/bdist.macosx-10.6-intel/egg/pysam/ctabix.py to ctabix.pyc byte-compiling build/bdist.macosx-10.6-intel/egg/pysam/TabProxies.py to TabProxies.pyc byte-compiling build/bdist.macosx-10.6-intel/egg/pysam/cvcf.py to cvcf.pyc creating build/bdist.macosx-10.6-intel/egg/EGG-INFO copying pysam.egg-info/PKG-INFO -> build/bdist.macosx-10.6-intel/egg/EGG-INFO copying pysam.egg-info/SOURCES.txt -> build/bdist.macosx-10.6-intel/egg/EGG-INFO copying pysam.egg-info/dependency_links.txt -> build/bdist.macosx-10.6-intel/egg/EGG-INFO copying pysam.egg-info/not-zip-safe -> build/bdist.macosx-10.6-intel/egg/EGG-INFO copying pysam.egg-info/requires.txt -> build/bdist.macosx-10.6-intel/egg/EGG-INFO copying pysam.egg-info/top_level.txt -> build/bdist.macosx-10.6-intel/egg/EGG-INFO writing build/bdist.macosx-10.6-intel/egg/EGG-INFO/native_libs.txt creating dist creating 'dist/pysam-0.7.7-py2.7-macosx-10.6-intel.egg' and adding 'build/bdist.macosx-10.6-intel/egg' to it removing 'build/bdist.macosx-10.6-intel/egg' (and everything under it) Creating /Users/umdp/Desktop/OpEx-1.0.0/tmp/lib/python2.7/site-packages/site.py Processing setuptools-0.6c11-py2.7.egg Copying setuptools-0.6c11-py2.7.egg to /Users/umdp/Desktop/OpEx-1.0.0/tmp/lib/python2.7/site-packages Adding setuptools 0.6c11 to easy-install.pth file Installing easy_install script to /Users/umdp/Desktop/OpEx-1.0.0/tmp/bin Installing easy_install-2.7 script to /Users/umdp/Desktop/OpEx-1.0.0/tmp/bin Installed /Users/umdp/Desktop/OpEx-1.0.0/tmp/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg Processing dependencies for setuptools==0.6c11 Finished processing dependencies for setuptools==0.6c11 Processing pysam-0.7.7-py2.7-macosx-10.6-intel.egg creating /Users/umdp/Desktop/OpEx-1.0.0/tmp/lib/python2.7/site-packages/pysam-0.7.7-py2.7-macosx-10.6-intel.egg Extracting pysam-0.7.7-py2.7-macosx-10.6-intel.egg to /Users/umdp/Desktop/OpEx-1.0.0/tmp/lib/python2.7/site-packages Adding pysam 0.7.7 to easy-install.pth file Installed /Users/umdp/Desktop/OpEx-1.0.0/tmp/lib/python2.7/site-packages/pysam-0.7.7-py2.7-macosx-10.6-intel.egg Processing dependencies for pysam==0.7.7 Searching for cython>=0.17 Reading http://pypi.python.org/simple/cython/ Best match: Cython 0.25.2 Downloading https://pypi.python.org/packages/b7/67/7e2a817f9e9c773ee3995c1e15204f5d01c8da71882016cac10342ef031b/Cython-0.25.2.tar.gz#md5=642c81285e1bb833b14ab3f439964086 Processing Cython-0.25.2.tar.gz Running Cython-0.25.2/setup.py -q bdist_egg --dist-dir /var/folders/t4/qklzmv9j4r35rwn9vf3xxc_00000gn/T/easy_install-hAJUyu/Cython-0.25.2/egg-dist-tmp-SWh2oh Unable to find pgen, not compiling formal grammar. warning: no files found matching '*.pyx' under directory 'Cython/Debugger/Tests' warning: no files found matching '*.pxd' under directory 'Cython/Debugger/Tests' warning: no files found matching '*.h' under directory 'Cython/Debugger/Tests' warning: no files found matching '*.pxd' under directory 'Cython/Utility' Adding Cython 0.25.2 to easy-install.pth file Installing cython script to /Users/umdp/Desktop/OpEx-1.0.0/tmp/bin Installing cygdb script to /Users/umdp/Desktop/OpEx-1.0.0/tmp/bin Installing cythonize script to /Users/umdp/Desktop/OpEx-1.0.0/tmp/bin Installed /Users/umdp/Desktop/OpEx-1.0.0/tmp/lib/python2.7/site-packages/Cython-0.25.2-py2.7-macosx-10.6-intel.egg Finished processing dependencies for pysam==0.7.7 ================================================================================ OpEx: Indexing genome by BWA ================================================================================ ./index_genome.sh: line 11: tools/bwa-0.5.10/bwa: No such file or directory ================================================================================ OpEx: Indexing genome by Stampy ================================================================================ Could not import the maptools module -- does the maptools.so library exist? Traceback (most recent call last): File "tools/stampy-1.0.14.1/stampy.py", line 14, in import maptools ImportError: No module named maptools Could not import the maptools module -- does the maptools.so library exist? Traceback (most recent call last): File "tools/stampy-1.0.14.1/stampy.py", line 14, in import maptools ImportError: No module named maptools ----------------------------------------- INSTALLING OPEX PIPELINE VERSION 1.0.0 ----------------------------------------- --------------------------------------------------------------------------------- Downloading and building components (BWA, Stampy, CoverView, Platypus, CAVA) ... --------------------------------------------------------------------------------- ------------------------------------ Adding default reference genome ... ------------------------------------ NOTE: the reference genome is being indexed by BWA and Stampy that will take a while. --------------------------------------------------- OPEX PIPELINE v1.0.0 INSTALLATION COMPLETED. Test installation: python test_installation.py ---------------------------------------------------