hanna cac04a407a For Manny: filter out reads where the the ref index == ... NO_ALIGNMENT_REFERENCE_INDEX but the alignment start != NO_ALIGNMENT_START. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1295 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-22 21:19:24 +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	For Manny: filter out reads where the the ref index ==	2009-07-22 21:19:24 +00:00
test/org/broadinstitute/sting	GLF rod as a AllelicVariant object.	2009-07-21 00:55:52 +00:00