Ryan Poplin d5f0848bd5 HC bam writer now sets the read to MQ0 if it isn't informative ... -- Makes visualization of read evidence easier in IGV.		2013-06-13 10:11:54 -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	HC bam writer now sets the read to MQ0 if it isn't informative	2013-06-13 10:11:54 -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	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