Guillermo del Angel 429800a192 Fix corner case rounding issue in MathUtils unit test: 10^logFactorial(4)) was 23.999999... which if cast directly yielded 23 - so, do pre-rounding to ensure correct integer result if caller will cast value.		2012-05-02 09:57:06 -04:00
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R	Add warning message about ratios in variantQCreport, give ratio for MAF > 10%	2012-04-25 12:22:32 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	…
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java	Fix corner case rounding issue in MathUtils unit test: 10^logFactorial(4)) was 23.999999... which if cast directly yielded 23 - so, do pre-rounding to ensure correct integer result if caller will cast value.	2012-05-02 09:57:06 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Remove unnecessary and obscure usage of old R	2012-05-01 13:39:09 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.	2012-04-17 14:22:48 -04:00
testdata	continuing the BQSR triage...	2012-04-05 14:34:15 -04:00