ebanks e05cb346f3 GenotypeLocusData now extends Variation. ... Also, Variations should be INSERTIONs or DELETIONs (and not just INDELs). Technically, VCF records can be indels now. More changes coming git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2150 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-24 21:07:55 +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/org/broadinstitute/sting	GenotypeLocusData now extends Variation.	2009-11-24 21:07:55 +00:00
test/org/broadinstitute/sting	BAM files created by TableRecalibration now have the version number and list of covariates used appended to their header with a new 'PG' tag. Eventually the entire list of command line args will be put in there as well. Big thanks to Matt and Aaron. The integration test uses the --no_pg_tag so that the md5 doesn't change every time the version number changes.	2009-11-24 20:53:57 +00:00