Guillermo del Angel 6c9d3ec155 Remerge after changes to allele construction code. More cleanups/fixes to artificial read pileup provider		2012-07-30 21:32:03 -04:00
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bqsr	Smoothing in the BQSR bins should be one error observation and one non-error observation.	2012-07-26 13:59:02 -04:00
compression/reducereads	Updating default value for -mindel to the one used by Khalid in the pipeline and me in my tests.	2012-07-10 02:04:26 -04:00
genotyper	Remerge after changes to allele construction code. More cleanups/fixes to artificial read pileup provider	2012-07-30 21:32:03 -04:00
haplotypecaller	Allele refactoring checkpoint #3: all integration tests except for PoolCaller are passing now. Fixed a couple of bugs from old code that popped up during md5 difference review. Added VariantContextUtils.requiresPaddingBase() method for tools that create alleles to use for determining whether or not to add the ref padding base. One of the HaplotypeCaller tests wasn't passing because of RankSumTest differences, so I added a TODO for Ryan to look into this.	2012-07-27 15:48:40 -04:00