Mark DePristo 752440707d AlignmentUtils.calcNumDifferentBases computes the number of bases that differ between a reference and read sequence given a cigar between the two.		2013-03-20 22:54:35 -04:00
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AlignmentUtilsUnitTest.java	AlignmentUtils.calcNumDifferentBases computes the number of bases that differ between a reference and read sequence given a cigar between the two.	2013-03-20 22:54:35 -04:00
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	New GATKSAMRecord concept of a strandless read, update to FS	2013-03-13 11:16:36 -04:00
MisencodedBaseQualityUnitTest.java	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00
ReadUtilsUnitTest.java	Fixed reported bug in BQSR for RNA seq alignments with Ns.	2013-03-14 11:26:52 -04:00