Ryan Poplin ac033ce41a Intermediate commit of new bubble assembly graph traversal algorithm for the HaplotypeCaller. Adding functionality for a path from an assembly graph to calculate its own cigar string from each of the bubbles instead of doing a massive Smith-Waterman alignment between the path's full base composition and the reference.		2013-01-31 11:32:19 -05:00
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AlignmentUtilsUnitTest.java	Intermediate commit of new bubble assembly graph traversal algorithm for the HaplotypeCaller. Adding functionality for a path from an assembly graph to calculate its own cigar string from each of the bubbles instead of doing a massive Smith-Waterman alignment between the path's full base composition and the reference.	2013-01-31 11:32:19 -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	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -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	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -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