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shasta 0.14.0-1
  • links: PTS, VCS
  • area: main
  • in suites: forky, sid
  • size: 29,636 kB
  • sloc: cpp: 82,262; python: 2,348; makefile: 222; sh: 143

Folder: scripts

d .. (parent)
- - rwxr-xr-x 1,106 AlignOrientedReads.py
- - rwxr-xr-x 942 AlignOrientedReads1.py
- - rwxr-xr-x 1,898 AlignOrientedReads4.py
- - rwxr-xr-x 958 AnalyzeAlignmentMatrix.py
- - rw-r--r-- 310 AnalyzeAssemblyGraphBubbles.py
- - rw-r--r-- 100 AnalyzeReadGraph.py
- - rwxr-xr-x 461 Assemble.py
- - rwxr-xr-x 810 AssembleMarkerGraphEdges.py
- - rwxr-xr-x 382 AssembleMarkerGraphVertices.py
- - rwxr-xr-x 1,234 AssembleSegment.py
- - rwxr-xr-x 651 CheckConfigurations.py
- - rwxr-xr-x 312 CheckMarkerGraphIsStrandSymmetric.py
- - rwxr-xr-x 719 CleanupDuplicateMarkers.py
- - rwxr-xr-x 937 CleanupRunDirectory.py
- - rwxr-xr-x 639 ClusterMarkerGraphEdgeOrientedReads.py
- - rwxr-xr-x 513 ColorGfaBySimilarityToSegment.py
- - rwxr-xr-x 148 ColorGfaKeySegments.py
- - rwxr-xr-x 687 ColorGfaWithTwoReads.py
- - rwxr-xr-x 1,892 ComputeAlignments.py
- - rwxr-xr-x 185 ComputeAssemblyStatistics.py
- - rwxr-xr-x 250 ComputeMarkerGraphCoverageHistogram.py
- - rwxr-xr-x 393 ComputeMarkerGraphVerticesCoverageData.py
- - rwxr-xr-x 241 ComputeReadGraphConnectedComponents.py
- - rwxr-xr-x 102 ComputeSortedMarkers.py
- - rwxr-xr-x 706 Copy.py
- - rwxr-xr-x 1,086 CopyDirectory.py
- - rw-r--r-- 137 CountKmers.py
- - rwxr-xr-x 1,504 CreateAndCleanupMarkerGraph.py
- - rwxr-xr-x 497 CreateAssembly.py
- - rwxr-xr-x 190 CreateAssemblyGraphEdges.py
- - rwxr-xr-x 228 CreateAssemblyGraphVertices.py
- - rwxr-xr-x 384 CreateCompressedAssemblyGraph.py
- - rwxr-xr-x 2,799 CreateConfigurationTable.py
- - rwxr-xr-x 901 CreateLocalSubgraph.py
- - rwxr-xr-x 283 CreateMarkerGraphAndTransitiveReduction.py
- - rwxr-xr-x 261 CreateMarkerGraphEdges.py
- - rwxr-xr-x 345 CreateMarkerGraphEdgesStrict.py
- - rwxr-xr-x 357 CreateMarkerGraphSecondaryEdges.py
- - rwxr-xr-x 847 CreateMarkerGraphVertices.py
- - rwxr-xr-x 1,376 CreateModules.py
- - rwxr-xr-x 378 CreatePrimaryMarkerGraphEdges.py
- - rwxr-xr-x 369 CreateReadGraph.py
- - rwxr-xr-x 761 CreateReadGraph2.py
- - rwxr-xr-x 365 CreateReadGraph3.py
- - rwxr-xr-x 369 CreateReadGraph4.py
- - rw-r--r-- 450 CreateReadGraphMode1.py
- - rwxr-xr-x 927 CreateReadGraphUsingPseudoPaths.py
- - rw-r--r-- 241 Detangle.py
- - rw-r--r-- 802 Detangle2.py
- - rwxr-xr-x 601 FastqGzToFasta.py
- - rwxr-xr-x 498 FastqToFasta.py
- - rwxr-xr-x 587 FastqToFastaAll.py
- - rwxr-xr-x 944 FindAlignmentCandidatesLowHash0.py
- - rwxr-xr-x 205 FindAssemblyGraphBubbles.py
- - rwxr-xr-x 273 FindMarkerGraphReverseComplementEdges.py
- - rwxr-xr-x 279 FindMarkerGraphReverseComplementVertices.py
- - rwxr-xr-x 91 FindMarkers.py
- - rwxr-xr-x 343 FlagChimericReads.py
- - rwxr-xr-x 351 FlagCrossStrandReadGraphEdges.py
- - rwxr-xr-x 431 FlagInconsistentAlignments.py
- - rwxr-xr-x 817 FlagPalindromicReads.py
- - rw-r--r-- 406 FlagPrimaryMarkerGraphEdges.py
- - rwxr-xr-x 5,022 GenerateConfig.py
- - rwxr-xr-x 4,900 GenerateFeedback.py
- - rwxr-xr-x 3,543 GenerateRandomHaplotypes.py
- - rwxr-xr-x 337 GetConfig.py
- - rwxr-xr-x 235 GetReadId.py
- - rwxr-xr-x 117 HistogramReadLength.py
- - rwxr-xr-x 3,633 InstallPrerequisites-Ubuntu-Old.sh
- - rwxr-xr-x 4,876 InstallPrerequisites-Ubuntu.py
- - rwxr-xr-x 398 InstallPrerequisites-Ubuntu.sh
- - rw-r--r-- 4,291 Mode2Assembly-A.py
- - rwxr-xr-x 1,511 Mode2Assembly-B-Prepare.py
- - rwxr-xr-x 2,819 Mode2Assembly-B.py
- - rw-r--r-- 750 Mode3Assembly.py
- - rwxr-xr-x 375 PruneMarkerGraphStrongSubgraph.py
- - rw-r--r-- 103 ReadGraphClustering.py
- - rw-r--r-- 280 RemoveReadGraphBridges.py
- - rwxr-xr-x 986 RestoreRun.py
- - rwxr-xr-x 2,961 RunAssemblies.py
- - rwxr-xr-x 859 SaveRun.py
- - rwxr-xr-x 1,046 SetMarkerGraphEdgeFlags.py
- - rwxr-xr-x 2,651 SetupRunDirectory.py
- - rwxr-xr-x 1,782 SetupSmallRunDirectory.py
- - rwxr-xr-x 2,135 SimpleBayesianConsensusCallerCreateBuiltin.py
- - rwxr-xr-x 538 SimplifyMarkerGraph.py
- - rwxr-xr-x 434 SplitMarkerGraphSecondaryEdges.py
- - rwxr-xr-x 808 StepSequence1.py
- - rwxr-xr-x 2,100 SummarizeAssemblies.py
- - rwxr-xr-x 68 Test.py
- - rw-r--r-- 139 TestSimpleBayesianConsensusCaller.py
- - rwxr-xr-x 645 TransitiveReduction.py
- - rwxr-xr-x 117 TravisCheckBuildMacOS.sh
- - rwxr-xr-x 233 TravisCheckBuildUbuntu.sh
- - rwxr-xr-x 1,426 WriteAlignmentCandidates.py
- - rwxr-xr-x 312 WriteAssemblyGraph.py
- - rwxr-xr-x 190 WriteBadMarkerGraphVertices.py
- - rwxr-xr-x 154 WriteFasta.py
- - rwxr-xr-x 183 WriteGfa.py
- - rwxr-xr-x 206 WriteGfaBothStrands.py
- - rwxr-xr-x 1,321 WriteLocalAlignmentCandidateReads.py
- - rwxr-xr-x 1,234 WriteLocalReadGraphReads.py
- - rwxr-xr-x 527 WriteMarkers.py
- - rwxr-xr-x 517 WriteOrientedRead.py
- - rwxr-xr-x 490 WriteOrientedReadPath.py
- - rwxr-xr-x 257 WriteOrientedReadsBySegment.py
- - rwxr-xr-x 122 WriteParallelMarkerGraphEdges.py
- - rwxr-xr-x 484 WritePseudoPath.py
- - rwxr-xr-x 338 WriteRead.py
- - rwxr-xr-x 1,002 WriteReadGraphEdges.py
- - rwxr-xr-x 121 WriteReads.py
- - rw-r--r-- 6,176 comparePhaseAssignments.py
- - rwxr-xr-x 626 dset64Test.py
- - rw-r--r-- 3,547 generateBandageLabelsFromAlignment.py
- - rw-r--r-- 1,362 testGlobalMsa.py