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	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
ArtificialSAMFileWriterUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
ArtificialSAMQueryIteratorUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
ArtificialSAMUtilsUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
GATKSAMRecordUnitTest.java	BitSet implementation of the on-the-fly recalibration using the CSV format file.	2012-03-16 13:02:15 -04:00
ReadUtilsUnitTest.java	Unit tests for GATKSAMRecord class	2012-01-26 17:06:36 -05:00