Mark DePristo c837d67b2f Merge pull request #273 from broadinstitute/rp_readIsPoorlyModelled ... Relaxing the constraints on the readIsPoorlyModelled function.		2013-06-13 08:40:24 -07:00
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genotyper	Relaxing the constraints on the readIsPoorlyModelled function.	2013-06-13 11:06:23 -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