Skip to content
Snippets Groups Projects
Select Git revision
  • biopet-bios
  • develop
  • epic-BIOPET-669
  • example-tarextract
  • fix-BIOPET-245
  • fix-BIOPET-593
  • fix-BIOPET-724
  • fix-BIOPET-728
  • fix-BIOPET-730
  • fix-BIOPET-782
  • gonl-GRCh38
  • master default
  • v0.9.0
  • v0.8.0
  • BIOS
  • v0.7.0
  • v0.6.0
  • v0.5.0
  • v0.4.0
  • v0.4.0-RC2
  • v0.4.0-RC1
  • v0.3.2
  • v0.3.1
  • v0.3.0
  • v0.2.0
  • start-feature-branching
  • v0.1.4
  • v0.1.2
  • v0.1.1
  • v0.1.0
  • 0.1.0
31 results
You can move around the graph by using the arrow keys.
Created with Raphaël 2.2.010Oct987630Sep29262217161512111098532129Aug28272625222019181514121187654130Jul29282724232221181514327Jun26232119171312109654327May2621201514Use 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 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 cases