Mark DePristo 9a29d6d4be Fix an catastrophic bug (WoW!) in the reference calculation of the UG ... -- The UG was using MathUtils binomial probability backward, so that the estimated confidence was always NaN, and was as a side effect other utils converted this to a meaningless 0.0. This is all because there wasn't a unit test. -- I've fixed the calculation, so it's now log10 based, uses robust MathUtils and QualityUtils functions to compute probabilities, and added a unit test.		2013-02-16 07:31:38 -08:00
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annotator	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
beagle	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
bqsr	PrintReads writes a header when used with -BQSR	2013-02-14 22:19:14 -05:00
compression/reducereads	Fixing the failing RR integration tests.	2013-02-06 12:40:56 -05:00
diagnostics	walker to calculate per base coverage distribution	2013-02-07 16:33:05 -05:00
diffengine	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
fasta	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
filters	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
genotyper	Fix an catastrophic bug (WoW!) in the reference calculation of the UG	2013-02-16 07:31:38 -08:00
haplotypecaller	Fixed non-determinism in HaplotypeCaller and some UG calls -	2013-02-12 15:43:29 -05:00
indels	Update MD5s to reflect version number change in the BAM header	2013-02-01 13:51:31 -05:00
phasing	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
validation	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
varianteval	Move some VCF/VariantContext methods back to the GATK based on feedback	2013-01-29 16:56:55 -05:00
variantrecalibration	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
variantutils	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00