ebanks 237ab1d489 1. As discussed in group meeting today, because we cap BQ by MQ, if MQ < minBQ then we filter the read. ... 2. Update to UGCalcLikelihoods for Chris: require a vcf bound to 'allele' to be provided so that we know exactly which alternate allele we should be calculating GLs for at each site. The user is warned when the VC is not biallelic or there are multiple records at a site. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4780 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-03 05:57:06 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	1. As discussed in group meeting today, because we cap BQ by MQ, if MQ < minBQ then we filter the read.	2010-12-03 05:57:06 +00:00
test	Bug fix in CountCovariates, skip over indel records as well as SNPs in the dbsnp file. CountCovariates is now called CountCovariatesWalker. I've always hated that the name was swapped.	2010-12-02 18:43:24 +00:00