Khalid Shakir 9801dd114f Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped ... The GATK -L unmapped is for GenomeLocs with SAMRecord.NO_ALIGNMENT_REFERENCE_NAME, not SAMRecord.getReadUnmappedFlag() Previously unmapped flag reads in the last bin were being printed while also seeking for the reads without a reference contig.		2012-04-27 09:58:38 -04:00
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AlignmentUtilsUnitTest.java	Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped	2012-04-27 09:58:38 -04:00
ArtificialPatternedSAMIteratorUnitTest.java	…
ArtificialSAMFileWriterUnitTest.java	…
ArtificialSAMQueryIteratorUnitTest.java	…
ArtificialSAMUtilsUnitTest.java	…
GATKSAMRecordUnitTest.java	…
ReadUtilsUnitTest.java	…