Hello,
since version 1.127 I am getting the following exception thrown
by BuildBamIndex:
Exception in thread "main" htsjdk.samtools.SAMException: Exception creating
BAM index for record XXXXX:00143:01038 131b aligned read.
at htsjdk.samtools.BAMIndexer.processAlignment(BAMIndexer.java:92)
at htsjdk.samtools.BAMIndexer.createIndex(BAMIndexer.java:291)
at htsjdk.samtools.BAMIndexer.createIndex(BAMIndexer.java:271)
at picard.sam.BuildBamIndex.doWork(BuildBamIndex.java:133)
at
picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187)
at
picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99)
Caused by: htsjdk.samtools.SAMException: BAM cannot be indexed without
setting a fileSource for record XXXXX:00143:01038 131b aligned read.
at
htsjdk.samtools.BAMIndexMetaData.recordMetaData(BAMIndexMetaData.java:130)
at
htsjdk.samtools.BAMIndexer$BAMIndexBuilder.processAlignment(BAMIndexer.java:182)
at htsjdk.samtools.BAMIndexer.processAlignment(BAMIndexer.java:90)
... 6 more
version 1.126 works fine and ValidateSamFile can't find anything wrong with
the bam.
I can send example files if necessary, even bam with a single read can
trigger the exception.
Any idea on what is going on ?
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