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Created with Raphaël 2.2.07Oct630Sep29262217161512111098532129Aug28272625222019181514121187654130Jul29282724232221181514327Jun26232119171312109654327May2621201514WipeReads docs wrap upAdd test for filteredBAM output in WipeReadsInitial complete main WipeReads function implementationAllow for .bam.bai or .bai extensionAdd initial BAM writing function in WipeReadsUpdate WipeReads test casesRefactor set-creating function to output set membership function in WipeReadsAdd more unit tests for WipeReadsUpdate WipeReads mate query to propagate exceptionsAdd tests for WipeReads overlap findersRefactor query interval builder for fewer BAM objectsRefactor set builder function in WipeReadsVarious small fixes for testingAdd function for set filtering in WipeReadsNest interval file parser functions and case classAdd algebird dependencyUpdate rrna01.bed test datasetUpdate access modifiers for WipeReads functionsUpdate enumerated strand optionsAdd initial functions to parse interval from fileUse Vector instead of Seq for multiple argument flag in WipeReadsUpdate WipeReads usage messageUse Seq instead of Array for immutability + easier comparisonFinalize WipeReads command line parser and its testsAdd .gitattributes fileAdd dependency for scalatestInitial app for WipeReadsRemove un deed lines for templateFix small bugsAdded defaults exampleChanged default to UnifiedGenotyperAdded UnifiedGenotyperAdded option to skip single sample callingReduce code duplicationYAMSVP pipeline updateMerge branch 'master' of git.lumc.nl:biopet/biopet into waiyiFix defaultsRemove comment out linesFix on defaultsRemove commented lines