Ryan Poplin ef1d58b7ff Bugfix for hom ref records that aren't GVCF blocks.		2013-09-29 19:19:26 -04:00
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genotyper	Relaxing the constraints on the readIsPoorlyModelled function.	2013-06-13 11:06:23 -04:00
gvcf	Bugfix for hom ref records that aren't GVCF blocks.	2013-09-29 19:19:26 -04:00
haplotype	Better caching for the HaplotypeCaller	2013-08-02 01:27:29 -04:00
haplotypeBAMWriter	Working version of HaplotypeCaller ReferenceConfidenceModel that accounts for indels as well as SNP confidences	2013-07-02 15:46:38 -04:00
nanoScheduler	A whole slew of improvements to the Haplotype Caller and related code.	2013-07-12 10:09:10 -04:00
pairhmm	Retreived PairHMM benchmarks from archive and made improvements	2013-08-28 17:23:35 -04:00
recalibration	Added hidden mode for BQSR to force all read groups to be the same one.	2013-05-06 19:09:10 -04:00
smithwaterman	New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points.	2013-05-13 09:36:39 -04:00
ContigComparatorUnitTest.java	Generalize and fixup ContigComparator	2013-02-09 09:52:13 -05:00