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
..
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	Cleanup and unit tests for QualityUtils	2013-02-16 07:31:37 -08:00
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