aaron 0513690416 two fixes in the new cached DbSNP code: ... -isBiallelic would incorrectly say triallelic sites are biallelic. -getAlternateAlleleList was broken, since the new cached list is immutable, we couldn’t remove list items. Also added a dbSNP validating walker to the one-offs, for testing the new b37 130 dbSNP rod. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2568 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-13 00:27:34 +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	two fixes in the new cached DbSNP code:	2010-01-13 00:27:34 +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