delangel cf9c9ae241 Three important updates for Dindel genotyper: ... a) Fix it up because it broke with a recent checkin to annotate vcf with unfiltered depth. b) Printout of ref/alt alleles in output vcf was incorrect because the start/stop positions of associated GenomeLoc were incorrectly computed in case of a deletion. c) Redid Beagle input/output walkers as not assume that ref was a single base, not to assume that variant was a vcf and generalized it to be indel-capable, so now the Beagle walkers can be used for indels as well. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4541 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-21 16:00:16 +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	Three important updates for Dindel genotyper:	2010-10-21 16:00:16 +00:00
test	Updated MD5s of VCFs, since the approximate command line arguments injected into the VCF headers now have a little more order to them thanks to changes in the ParsingEngine.	2010-10-21 03:07:40 +00:00