Guillermo del Angel 9686e91a51 Added small feature to VariantFiltration to filter sites outside of a given mask: ... -- Sometimes it's desireable to specify a set of "good" regions and filter out other stuff (like say an alignability mask or a "good regions" mask). But by default, the -mask argument in VF will only filter sites inside a particular mask. New argument -filterNotInMask will reverse default logic and filter outside of a given mask. -- Added integration test, and made sure we also test with a BED rod.		2013-03-31 08:48:16 -04:00
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java	Added small feature to VariantFiltration to filter sites outside of a given mask:	2013-03-31 08:48:16 -04:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00