Valentin Ruano-Rubio 98ffcf6833 Get gVCF to work without --dontTrimActiveRegions ... Story: https://www.pivotaltracker.com/story/show/65048706 https://www.pivotaltracker.com/story/show/65116908 Changes: ActiveRegionTrimmer in now an argument collection and it returns not only the trimmed down active region but also the non-variant containing flanking regions HaplotypeCaller code has been simplified significantly pushing some functionality two other classes like ActiveRegion and AssemblyResultSet. Fixed a problem with the way the trimming was done causing some gVCF non-variant records no have conservative 0,0,0 PLs		2014-02-05 22:50:45 -05:00
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gatk-protected	Get gVCF to work without --dontTrimActiveRegions	2014-02-05 22:50:45 -05:00
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
pom.xml	Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script.	2014-02-03 13:50:46 -05:00