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Created with Raphaël 2.2.014Oct1310987630Sep29262217161512111098532129Aug28272625222019181514121187654130Jul29282724232221181514327Jun26232119171312109654327May2621201514Fix missing variantsAdd VcfToTsvFix missed refactor (issue #29)Reorganize toolsMerge branch 'peter' into 'master'Fix argsAdded CheckAllelesVcfInBamFix argsRemoved unused importMerge branch 'bow' into 'master'Merge branch 'waiyi' into 'master'Merge from masterAdding tophatUse TestNGSuite and Matchers in Ln command testUse TestNGSuite and Matchers in WipeReads testUse common CLI argument parser for WipeReadsNetbeans configurations on formatting using CheckStyle pluginRemoving unused dependencyMerge commit '243fd59aa7e2cd3600a215bca2a4a53864423adb'Switched to ToolCommand args parsingChanged name to commandNameUpdate general argument parsingSet default validation stringency to lenient in WipeReadsMore unit test for WipeReadsUnused function & comments cleanup in WipeReadsAdded scopts library and log4j to ToolCommandsUse orestes.bloomfilter instead of com.twitter.algebird for Bloom filter implementationUpdate returned filter function in WipeReads to use SAMRecords onlyAutomatic class name conversionAutomatic class name conversionRefactor 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 value