I'm having some issues viewing BAM files generated by bwa bwasw and samtools (versions 0.5.9-r16 and 0.1.17, respectively). I generated them the usual way, e.g.:
bwa bwasw speciesA.hap_1.fa assembla_1.flanks.fa | samtools view -bS - | samtools sort - assembla_1.flanks.fa_hap1
When I load them in IGV (2.0.7), I'm able to view a few alignments, but then I repeatedly get an error dialog, with messages like this to the console:
ERROR [2011-08-12 13:57:54,675] [AlignmentDataManager.java:355] [pool-2-thread-2] Error loading alignments
org.broad.igv.exceptions.DataLoadException: <html>An error occurred while accessing: Error: java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -92<br>
at org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:341)
at org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:182)
at org.broad.igv.sam.CachingQueryReader.query(CachingQueryReader.java:122)
at org.broad.igv.sam.AlignmentDataManager$2.run(AlignmentDataManager.java:330)
at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:74)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:619)
ERROR [2011-08-12 13:57:55,525] [CachingQueryReader.java:340] [pool-2-thread-1] Error loading alignment data
java.lang.IllegalArgumentException: Bad byte passed to charToCompressedBase: -92
at net.sf.samtools.SAMUtils.compressedBaseToByteHigh(SAMUtils.java:199)
at net.sf.samtools.SAMUtils.compressedBasesToBytes(SAMUtils.java:85)
at net.sf.samtools.BAMRecord.decodeReadBases(BAMRecord.java:333)
at net.sf.samtools.BAMRecord.getReadBases(BAMRecord.java:263)
at net.sf.samtools.SAMRecord.getReadString(SAMRecord.java:194)
at org.broad.igv.sam.SamAlignment.<init>(SamAlignment.java:115)
at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:50)
at org.broad.igv.sam.reader.WrappedIterator.next(WrappedIterator.java:33)
at org.broad.igv.sam.CachingQueryReader.loadTiles(CachingQueryReader.java:236)
at org.broad.igv.sam.CachingQueryReader.getTiles(CachingQueryReader.java:182)
at org.broad.igv.sam.CachingQueryReader.query(CachingQueryReader.java:122)
at org.broad.igv.sam.AlignmentDataManager$2.run(AlignmentDataManager.java:330)
at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:74)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:619)
Thanks for any info you might be able to provide!
Rod