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Created with Raphaël 2.2.028Aug2726252423222120191817161514131211643130Jul28272423222117167632130Jun292827262524232221191716151098765432129May28272619181413121110974130Apr2928232016151413Merge branch 'develop' into feature-option_keep_files_flexiprepVarious style fixesMpileupToVcfTestMerge branch 'fix-picard' into 'develop' Merge branch 'feature-tool_squish_bed' into 'develop' Resources for checkVCfInBamMerge branch 'develop' into tooltestsFindRepeatsPacBioTestRemove squish bed python scriptSwitch to squishBed toolAdded squish bed extensionMore message fixesFastqSplitterTestFastqSplitter optparser messages correctionMerge branch 'feature-region_af_count' into 'develop' Merge branch 'fix-aligners' into 'develop' Added picard R scipts as workaround till issue is resolvedCode style fixChange val nameAdded a method to validate contigsChange to BedRecordsList for scatteringAdded test to check for overlap between scattersAdding method to test scatterAdding method to test scatterAdded fromReference methodfixed commandAdding a scatter methodCheckAllelesVcfInBam testing.small refactor: method name correctionBiopetFlagStat testingAdded option to suply fasta file as seperated fasta filesRaised memory for starMerge branch 'fix-tophat_unittests' into 'develop' Fixed tophat unittestsMerge remote-tracking branch 'origin/develop' into feature-region_af_countMerge remote-tracking branch 'origin/develop' into feature-option_keep_files_flexiprepFixed testingMerge branch 'fix-aligners' into 'develop' Merge branch 'fix-index_output_mergeSam' into 'develop' changed error to warn