Eric Banks b53336c2d0 Added hidden mode for BQSR to force all read groups to be the same one. ... * Very useful for debugging sample-specific issues * This argument got lost in the transition from BQSR v1 to v2 * Added unit test to cover this case		2013-05-06 19:09:10 -04:00
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genotyper	Extended the allele-biased down-sampling functionality to handle reduced reads.	2013-04-26 11:23:17 -04:00
haplotype	LD-based merging algorithm for nearby events in the haplotypes	2013-04-08 12:47:48 -04:00
haplotypeBAMWriter	Slightly improved Smith-Waterman parameter values for HaplotypeCaller Path comparisons	2013-04-11 18:22:55 -04:00
nanoScheduler	Fix caching indices in the PairHMM	2013-04-08 11:05:12 -04:00
pairhmm	Fix caching indices in the PairHMM	2013-04-08 11:05:12 -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	Slightly improved Smith-Waterman parameter values for HaplotypeCaller Path comparisons	2013-04-11 18:22:55 -04:00
ContigComparatorUnitTest.java	Generalize and fixup ContigComparator	2013-02-09 09:52:13 -05:00