Valentin Ruano-Rubio 748d2fdf92 Added Integration test to verify the bugs are not there anymore as reported in pivotracker		2014-01-26 23:29:31 -05:00
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collections	Adding Graph-based likelihood ratio calculation to HC	2013-12-02 19:37:19 -05:00
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	Fix for the PairHMM transition probability miscalculation.	2014-01-26 16:30:36 -05:00
pairhmm	Added Integration test to verify the bugs are not there anymore as reported in pivotracker	2014-01-26 23:29:31 -05:00
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
RandomDNA.java	Adding Graph-based likelihood ratio calculation to HC	2013-12-02 19:37:19 -05:00