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Created with Raphaël 2.2.017Jan1514121110865430Dec29282625242322211817161514131110764330Nov29272625242320191817161211109876543231Oct302928272625232221201916151413129876Merge branch 'feature-core_unit_tests' into 'develop' Merge branch 'fix-renames' into 'develop' Rename camel caps to underscoreUnify output bam namesbgzip piping went wrong fix with if stdout else >Fix output path for pindel (pindel outputs to certain dir with prefix_)generate dir for varscanFix output path for pindel (pindel outputs to certain dir with prefix_)Our option couln't be -l (due to biopet debug flag)add varscan to shiva variantcallersChanged defaults and fix the pindelconfig script.Added test to summary coreFix major error, things in beforeCmd was intended to do in beforeGraphFix pindel caller (fixing null error with Option[File] = None instead of _)Fix input of bams to svcalling tools..Adding empty summary testOptimize importsAdding tests for input files for summaryAdd test addSummarizableAdded simple test for summaryQscriptAdded test for summarizableFixed reference testFix compile errorsAdding Pindel to ShivaSVCallingMerge remote-tracking branch 'remotes/origin/develop' into feature-measure_modulesMerge branch 'feature-gentrap_report' into 'develop' Merge branch 'fix-spelling-errors_2016-jan' into 'develop' Added annotation traitsFix spelling error in the WriteDependencies JSON outputAdding the pindel wrapper to the extensions. Updated to support v0.2.5b8Added empty implementationsStyle fixesAdded more fieldsFix metricsMerge branch 'fix-toucan' into 'develop' Fix short nameAdded rnaFix labelsAdded rna metrics plotOnly show wgs if executed