Eric Banks ba2c3b57ed Extended the allele-biased down-sampling functionality to handle reduced reads. ... Note that this works only in the case of pileups (i.e. coming from UG); allele-biased down-sampling for RR just cannot work for haplotypes. Added lots of unit tests for new functionality.		2013-04-26 11:23:17 -04:00
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AlignmentUtilsUnitTest.java	Major improvements to HC that trims down active regions before genotyping	2013-04-08 12:47:49 -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	Extended the allele-biased down-sampling functionality to handle reduced reads.	2013-04-26 11:23:17 -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