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Created with Raphaël 2.2.08Oct7630Sep29262217161512111098532129Aug28272625222019181514121187654130Jul29282724232221181514327Jun26232119171312109654327May2621201514Refactor codeMerge branch 'feat_wipereads' into 'master'Update retrieveCommand functionMake sure WipeReads also checks for single reads when filtering + writingUpdate main interfaceOptimize set building in WipeReads by bypassing mate lookupSimplify WipeReads usage messageImprove mate query to better-disambiguate multiple-mapped readsMerge overlapping intervals prior to making QueryIntervalSimplify ToolCommand.toolName valueRemove strand option in WipeReadsAdd explicit system exit points in main jarFix typoAdd WipeReads to main command line interfaceImprove main command line interfaceCreate interval tree map lazily in WipeReadsUpdate WipeReads to take splicing structure into account when finding overlapsUpdate SAMRecord equality test to test as file is iteratedCode reformat + unused import removal in WipeReadsWipeReads 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 WipeReads