Invalid .bam files?

[ay...@grailbio.com]

Hi all,

I have been using the biogo library, and it's really great for what I need, but when I produced some output bam files using hts.bam.Wrtier, I encountered some errors.  I may be doing something wrong here, but when I run the output bam file through a checker like this:

$ sambamba_v0.6.6 index -c small-mine-dups.bam

I often get an error like this regarding the indices:

sambamba-index: Bin in read with name 'SN1279:510:C8EL3ANXX:4:1315:17239:8943' is set incorrectly (4680 instead of expected 4900)

And when I then read in the same bam file through biogo's Reader, some of the records do not come through.

I then tested the same bam file using picard, and I also get some error reports like this:

$ picard ValidateSamFile I=small-mine-dups.bam MODE=SUMMARY

[Mon Jul 24 14:02:48 PDT 2017] picard.sam.ValidateSamFile INPUT=small-mine-dups.bam MODE=SUMMARY    MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json

[Mon Jul 24 14:02:48 PDT 2017] Executing as ayip@ayip on Linux 4.10.0-27-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_131-b11; Picard version: 2.10.3-SNAPSHOT

## HISTOGRAM    java.lang.String

Error Type      Count

ERROR:INVALID_INDEXING_BIN      941

ERROR:INVALID_INDEX_FILE_POINTER        1

ERROR:MISSING_PLATFORM_VALUE    155

[Mon Jul 24 14:02:52 PDT 2017] picard.sam.ValidateSamFile done. Elapsed time: 0.06 minutes.

Runtime.totalMemory()=1242038272

To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp

Does this seem like a bug in biogo, or could I be using the library incorrectly?

thanks, Alex

[Dan Kortschak]

Please file an issue on the tracker, including a minimal reproducer or
the exact steps you went through to achieve the error (former is
preferred).

thanks
Dan

[ay...@grailbio.com]

I just filed https://github.com/biogo/hts/issues/101

Thanks for looking into it!

- Alex