asivache a138bad95a A rare but not-so-subtle bug fixed: a funky alignment (a kind that should not have been generated in the first place) could make the indel left-adjusting method to overshoot read start and build a cigar like -3M6I... ... also, few minor fix-ups. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2567 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-12 21:29:50 +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	A rare but not-so-subtle bug fixed: a funky alignment (a kind that should not have been generated in the first place) could make the indel left-adjusting method to overshoot read start and build a cigar like -3M6I...	2010-01-12 21:29:50 +00:00
test/org/broadinstitute/sting	The recalibrator now uses all input RODs when looking for known polymorphic sites not just the one named dbsnp. Added an integration test which uses both dbsnp and an input vcf file and skips over the union of the two.	2010-01-12 18:50:39 +00:00