Christopher Hartl ba8622ff0d number of stashed changes are lurking in here. In order of importance: ... - Fix for M_Trieb's error report on the forum, and addition of integration tests to cover the walker. - Addition of StructuralIndel as a class of variation within the VariantContext. These are for variants with a full alt allele that's >150bp in length. - Adaptation of the MVLikelihoodRatio to work for a set of trios (takes the max over the trios of the MVLR) - InsertSizeDistribution changed to use the new gatk report output (it was previously broken) - RetrogeneDiscovery changed to be compatible with the new gatk report - A maxIndelSize argument added to SelectVariants - ByTranscriptEvaluator rewritten for cleanliness - VariantRecalibrator modified to not exclude structural indels from recalibration if the mode is INDEL - Documentation added to DepthOfCoverageIntegrationTest (no, don't yell at chartl ;_; ) Also sorry for the long commit history behind this that is the result of fixing merge conflicts. Because this *also* fixes a conflict (from git stash apply), for some reason I can't rebase all of them away. I'm pretty sure some of the commit notes say "this note isn't important because I'm going to rebase it anyway".		2012-08-21 07:08:58 -04:00
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broadinstitute/sting	number of stashed changes are lurking in here. In order of importance:	2012-08-21 07:08:58 -04:00