Christopher Hartl 944a7d815e Bringing VQSRV3 up to date. Lots of new features (un-classifying the worst-performing training sites, treating the x% best/worst sites as postive/negative points, ability to pass in a monomorphic track to see ROC curves output). Minor changes to AlleleBalance: weighted average was incorrectly specified (using logscale actually biased the average towards the AB of low-quality genotypes), and breaking out AB by het, hom, and diploid to bring it in line with some (private) changes to the indel likelihood model that (correctly) computes these values for indels.		2012-04-28 11:31:03 -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	…
doc	…
java	Bringing VQSRV3 up to date. Lots of new features (un-classifying the worst-performing training sites, treating the x% best/worst sites as postive/negative points, ability to pass in a monomorphic track to see ROC curves output). Minor changes to AlleleBalance: weighted average was incorrectly specified (using logscale actually biased the average towards the AB of low-quality genotypes), and breaking out AB by het, hom, and diploid to bring it in line with some (private) changes to the indel likelihood model that (correctly) computes these values for indels.	2012-04-28 11:31:03 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
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