Mauricio Carneiro 371ea2f24c Fixed IndelRealigner reference length bug (GSA-774) ... -- modified ReadBin GenomeLoc to keep track of softStart() and softEnd() of the reads coming in, to make sure the reference will always be sufficient even if we want to use the soft-clipped bases -- changed the verification from readLength to aligned bases to allow reads with soft-clipped bases -- switched TreeSet -> PriorityQueue in the ConstrainedMateFixer as some different reads can be considered equal by picard's SAMRecordCoordinateComparator (the Set was replacing them) -- pulled out ReadBin class so it can be testable -- added unit tests for ReadBin with soft-clips -- added tests for getMismatchCount (AlignmentUtils) to make sure it works with soft-clipped reads GSA-774 #resolve		2013-02-19 16:00:36 -05:00
..
AlignmentUtilsUnitTest.java	Fixed IndelRealigner reference length bug (GSA-774)	2013-02-19 16:00:36 -05:00
ArtificialBAMBuilderUnitTest.java	Last manual license update (hopefully)	2013-01-18 16:13:07 -05:00
ArtificialPatternedSAMIteratorUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
ArtificialSAMFileWriterUnitTest.java	PrintReads writes a header when used with -BQSR	2013-02-14 22:19:14 -05:00
ArtificialSAMQueryIteratorUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
ArtificialSAMUtilsUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
ArtificialSingleSampleReadStreamUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
GATKSAMRecordUnitTest.java	PileupElement and LIBS cleanup	2013-01-11 15:17:17 -05:00
MisencodedBaseQualityUnitTest.java	Need to reset the static counter before tests are run or else we won't be deterministic.	2013-02-05 10:41:46 -05:00
ReadUtilsUnitTest.java	Move BaseUtils back to the GATK by request, along with associated utility methods	2013-01-30 13:09:44 -05:00