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Created with Raphaël 2.2.07Oct630Sep29262217161512111098532129Aug28272625222019181514121187654130Jul29282724232221181514327Jun26232119171312109654327May2621201514Update 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 linesFix ArgumentsFix output dirsmove recalibration to final fileadded defaul ploidychanged defaultsAdded memory limit optionAdded ploidy optionFix genotyping on deleted bases