diff --git a/addCopyrights-BuildData.pl b/addCopyrights-BuildData.pl index 1b8638abf..941baa377 100644 --- a/addCopyrights-BuildData.pl +++ b/addCopyrights-BuildData.pl @@ -37,6 +37,7 @@ $stoppingCommits{"9e9bd674b705f89817b07ff30067210c2d180f42"} = 1; # 14 AUG 2017 $stoppingCommits{"0fff8a511fd7d74081d94ff9e0f6c0351650ae2e"} = 1; # 27 FEB 2018 - v1.7 $stoppingCommits{"fcc3fe19eb635abd735486d215fbf65c56bcf4ee"} = 1; # 22 OCT 2018 - v1.8 +$stoppingCommits{"438412092d4470c63323f20780252b48ec132d44"} = 1; # 04 NOV 2019 - v1.9 open(F, "< logs") or die "Failed to open 'logs': $!\n"; @@ -68,6 +69,10 @@ $author = "Brian P. Walenz"; } elsif (m/koren/i) { $author = "Sergey Koren"; + } elsif (m/nurk/i) { + $author = "Sergey Nurk"; + } elsif (m/rhie/i) { + $author = "Arang Rhie"; } else { print STDERR "Skipping commit from '$_'\n"; $author = undef; diff --git a/addCopyrights.dat b/addCopyrights.dat index 2662f2f65..59e65c156 100644 --- a/addCopyrights.dat +++ b/addCopyrights.dat @@ -15460,3 +15460,762 @@ D src/sequence/sequence-summarize.C src/sequence/sequence.C D src/sequence/sequence.H src/sequence/sequence.C D src/utility/edlib.C src/overlapInCore/libedlib/edlib.C D src/utility/edlib.H src/overlapInCore/libedlib/edlib.H +A src/pipelines/canu/Defaults.pm nihh20191104Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20191101Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20191101Brian P. Walenz +A src/pipelines/canu/Grid_DNANexus.pm nihh20191101Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20191101Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20191024Brian P. Walenz +A src/pipelines/canu/Grid_DNANexus.pm nihh20191027Brian P. Walenz +A src/pipelines/canu/Grid_DNANexus.pm nihh20191027Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20191025Sergey Koren +A src/pipelines/canu/Execution.pm nihh20191025Sergey Koren +A src/pipelines/canu/Configure.pm nihh20191019Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20191023Brian P. Walenz +A src/bogart/AS_BAT_OptimizePositions.C nihh20191018Brian P. Walenz +A src/bogart/AS_BAT_BestOverlapGraph.C nihh20191017Brian P. Walenz +A src/overlapBasedTrimming/trimReads-largestCovered.C nihh20191008Brian P. Walenz +A src/pipelines/canu/Grid_PBSTorque.pm nihh20191016Sergey Koren +A src/bogart/AS_BAT_Logging.C nihh20191016Brian P. Walenz +A src/bogart/AS_BAT_Logging.H nihh20191016Brian P. Walenz +A src/bogart/AS_BAT_OptimizePositions.C nihh20191016Brian P. Walenz +A src/bogart/bogart.C nihh20191016Brian P. Walenz +A buildRelease-DNAnexus.sh nihh20191016Brian P. Walenz +A src/pipelines/dx-canu/dxapp.json nihh20191016Brian P. Walenz +A src/pipelines/dx-canu/src/canu-job-launcher.sh nihh20191016Brian P. Walenz +A src/pipelines/dx-trio/.gitignore nihh20191016Brian P. Walenz +A src/pipelines/dx-trio/dxapp.json nihh20191016Brian P. Walenz +A src/pipelines/dx-trio/resources/bin/dx-get-instance-info.py nihh20191016Brian P. Walenz +A src/pipelines/dx-trio/src/canu-job-launcher.sh nihh20191016Brian P. Walenz +A buildRelease-DNAnexus.sh nihh20191015Brian P. Walenz +A src/Makefile nihh20191015Brian P. Walenz +A src/dx-canu/dxapp.json nihh20191015Brian P. Walenz +A src/dx-canu/src/canu-job-launcher.sh nihh20191015Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20191015Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20191015Brian P. Walenz +A src/pipelines/canu.pl nihh20191014Sergey Koren +A src/pipelines/canu/Defaults.pm nihh20191014Sergey Koren +A src/pipelines/canu/OverlapMhap.pm nihh20191014Sergey Koren +A src/pipelines/canu/Configure.pm nihh20191014Sergey Koren +A src/pipelines/canu/OverlapErrorAdjustment.pm nihh20191014Sergey Koren +A src/bogart/AS_BAT_BestOverlapGraph.C nihh20191014Sergey Koren +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20191014Sergey Koren +A src/overlapErrorAdjustment/correctOverlaps.C nihh20191014Sergey Koren +A src/overlapErrorAdjustment/correctOverlaps.H nihh20191014Sergey Koren +A buildRelease-DNAnexus.sh nihh20191011Brian P. Walenz +A src/dx-canu/dxapp.json nihh20191011Brian P. Walenz +A src/dx-canu/src/canu-job-launcher.sh nihh20191011Brian P. Walenz +A src/pipelines/canu.pl nihh20191011Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20191011Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20191011Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20191011Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20191011Brian P. Walenz +A src/pipelines/canu/OverlapMhap.pm nihh20191011Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20191011Brian P. Walenz +A src/pipelines/canu/Report.pm nihh20191011Brian P. Walenz +A src/pipelines/canu/SequenceStore.pm nihh20191011Brian P. Walenz +A src/pipelines/canu/OverlapMMap.pm nihh20191011Brian P. Walenz +A src/pipelines/object-store-simulator.pl nihh20191011Brian P. Walenz +A src/utility/objectStore.C nihh20191011Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20191007Brian P. Walenz +A src/Makefile nihh20191007Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20191003Sergey Koren +A src/pipelines/canu/OverlapErrorAdjustment.pm nihh20191003Sergey Koren +A src/stores/ovStore.C nihh20191002Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C nihh20191002Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20191002Sergey Nurk +A src/overlapErrorAdjustment/correctionOutput.H nihh20191002Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C nihh20191002Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Output.C nihh20191002Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C nihh20191002Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Output.C nihh20191002Sergey Nurk +A src/overlapErrorAdjustment/findErrors.H nihh20191002Sergey Nurk +A src/stores/ovStore.C nihh20191002Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20191002Sergey Nurk +A src/main.mk nihh20191002Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C nihh20191001Sergey Koren +A src/utgcns/unitigConsensus.C nihh20190927Sergey Koren +A src/overlapErrorAdjustment/findErrors.H nihh20190927Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C nihh20190927Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20190927Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C nihh20190927Sergey Nurk +A src/utgcns/libpbutgcns/AlnGraphBoost.C nihh20190926Sergey Koren +A src/utgcns/libpbutgcns/AlnGraphBoost.C nihh20190925Sergey Koren +A src/utgcns/unitigConsensus.C nihh20190925Sergey Koren +A src/overlapErrorAdjustment/findErrors-Read_Frags.C nihh20190926Sergey Koren +A src/overlapErrorAdjustment/findErrors.H nihh20190926Sergey Koren +A src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C nihh20190926Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C nihh20190926Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20190926Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Output.C nihh20190925Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C nihh20190924Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C nihh20190924Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Output.C nihh20190924Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C nihh20190923Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20190923Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Output.C nihh20190923Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Process_Olap.C nihh20190923Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C nihh20190918Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20190918Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Process_Olap.C nihh20190918Sergey Nurk +A src/stores/ovStore.C nihh20190918Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20190916Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20190913Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20190912Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20190911Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C nihh20190909Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20190909Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C nihh20190906Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Prefix_Edit_Distance.C nihh20190905Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20190905Sergey Nurk +A src/overlapErrorAdjustment/correctionOutput.H nihh20190905Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C nihh20190905Sergey Nurk +A src/overlapErrorAdjustment/findErrors.H nihh20190905Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Output.C nihh20190828Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Output.C nihh20190823Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C nihh20190823Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20190823Sergey Nurk +A src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C nihh20190823Sergey Nurk +A src/overlapErrorAdjustment/correctionOutput.H nihh20190823Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C nihh20190823Sergey Nurk +A src/overlapErrorAdjustment/correctionOutput.H nihh20190823Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C nihh20190823Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Output.C nihh20190823Sergey Nurk +A src/overlapErrorAdjustment/correctionOutput.H nihh20190822Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C nihh20190822Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Output.C nihh20190822Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C nihh20190822Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Output.C nihh20190822Sergey Nurk +A src/overlapErrorAdjustment/findErrors.H nihh20190822Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Output.C nihh20190822Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C nihh20190822Sergey Nurk +A src/Makefile nihh20190815Sergey Nurk +A src/overlapErrorAdjustment/analyzeAlignment.C nihh20190815Sergey Nurk +A src/overlapErrorAdjustment/analyzeAlignment.H nihh20190815Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Analyze_Alignment.C nihh20190815Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Output.C nihh20190815Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Process_Olap.C nihh20190815Sergey Nurk +A src/overlapErrorAdjustment/findErrors.H nihh20190815Sergey Nurk +A src/bogart/AS_BAT_DetectSpurs.C nihh20190926Brian P. Walenz +A src/bogart/AS_BAT_DetectSpurs.H nihh20190926Brian P. Walenz +A src/bogart/bogart.C nihh20190926Brian P. Walenz +A src/bogart/bogart.mk nihh20190926Brian P. Walenz +A src/stores/ovStore.C nihh20190926Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190927Sergey Koren +A src/utgcns/libpbutgcns/AlnGraphBoost.C nihh20190926Sergey Koren +A src/utgcns/libpbutgcns/AlnGraphBoost.C nihh20190925Sergey Koren +A src/utgcns/unitigConsensus.C nihh20190925Sergey Koren +A src/pipelines/canu/Grid_Cloud.pm nihh20190918Brian P. Walenz +A src/pipelines/object-store-simulator.pl nihh20190918Brian P. Walenz +A src/canu_version_update.pl nihh20190903Brian P. Walenz +A src/utility/files.C nihh20190827Brian P. Walenz +A src/utility/files.H nihh20190827Brian P. Walenz +A src/pipelines/canu/Consensus.pm nihh20190903Brian P. Walenz +A src/pipelines/canu/Grid_LSF.pm nihh20190829Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20190829Brian P. Walenz +A src/pipelines/canu/Grid_Slurm.pm nihh20190829Brian P. Walenz +A src/Makefile nihh20190827Brian P. Walenz +A src/sequence/sequence-simulate.C nihh20190827Brian P. Walenz +A src/sequence/sequence.C nihh20190827Brian P. Walenz +A src/sequence/sequence.H nihh20190827Brian P. Walenz +A src/sequence/share/pacbio nihh20190827Brian P. Walenz +A src/sequence/share/pacbio-hifi nihh20190827Brian P. Walenz +A src/sequence/share/ultra-long-nanopore nihh20190827Brian P. Walenz +A src/sequence/sequence-simulate.C nihh20190827Brian P. Walenz +A src/utility/sampledDistribution.H nihh20190827Brian P. Walenz +A src/overlapErrorAdjustment/findErrors-Output.C nihh20190816Sergey Nurk +A src/overlapErrorAdjustment/findErrors-Output.C nihh20190815Brian P. Walenz +A src/pipelines/canu/Grid_LSF.pm nihh20190814Brian P. Walenz +A src/pipelines/canu/Grid_LSF.pm nihh20190814Brian P. Walenz +A src/pipelines/canu-time.pl nihh20190814Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20190814Brian P. Walenz +A src/utility/files-buffered-implementation.H nihh20190814Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20190730Sergey Koren +A src/pipelines/canu/OverlapMhap.pm nihh20190730Brian P. Walenz +A src/bogart/AS_BAT_OptimizePositions.C nihh20190727Brian P. Walenz +A src/bogart/AS_BAT_OptimizePositions.C nihh20190727Brian P. Walenz +A src/pipelines/canu.pl nihh20190724Sergey Koren +A src/pipelines/canu/Unitig.pm nihh20190724Brian P. Walenz +A src/pipelines/canu/Unitig.pm nihh20190724Brian P. Walenz +A documentation/source/parameter-reference.rst nihh20190724Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20190724Brian P. Walenz +A src/utility/files.C nihh20190723Brian P. Walenz +A src/stores/ovStoreFile.C nihh20190723Brian P. Walenz +A src/stores/sqStore.C nihh20190719Brian P. Walenz +A src/pipelines/canu/Grid_SGE.pm nihh20190719Brian P. Walenz +A src/overlapAlign/computeAlignments.C nihh20190719Brian P. Walenz +A src/overlapAlign/overlapAlign.C nihh20190719Brian P. Walenz +A src/overlapAlign/computeAlignments.C nihh20190718Sergey Koren +A src/overlapAlign/overlapAlign.C nihh20190718Sergey Koren +A src/pipelines/canu/Defaults.pm nihh20190717Sergey Koren +A src/stores/sqStoreCreate.C nihh20190717Sergey Koren +A src/stores/sqStoreCreate.C nihh20190717Sergey Koren +A documentation/source/conf.py nihh20190715Brian P. Walenz +A src/canu_version_update.pl nihh20190715Brian P. Walenz +A src/correction/falconsense.C nihh20190715Brian P. Walenz +A src/gfa/alignGFA.C nihh20190715Brian P. Walenz +A src/stores/tgStore.C nihh20190715Brian P. Walenz +A src/stores/tgStoreDump.C nihh20190715Brian P. Walenz +A src/stores/tgStoreFilter.C nihh20190715Brian P. Walenz +A src/stores/tgStoreLoad.C nihh20190715Brian P. Walenz +A src/stores/tgTig.C nihh20190715Brian P. Walenz +A src/stores/tgTig.H nihh20190715Brian P. Walenz +A src/stores/tgTigMultiAlignDisplay.C nihh20190715Brian P. Walenz +A src/stores/tgTigSizeAnalysis.C nihh20190715Brian P. Walenz +A src/stores/tgTigSizeAnalysis.H nihh20190715Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190715Brian P. Walenz +A src/utgcns/utgcns.C nihh20190715Brian P. Walenz +A src/bogart/AS_BAT_Outputs.C nihh20190715Brian P. Walenz +A src/main.mk nihh20190715Brian P. Walenz +A src/pipelines/canu/Consensus.pm nihh20190715Brian P. Walenz +A src/stores/tgStore.H nihh20190715Brian P. Walenz +A src/stores/tgStoreDump.C nihh20190715Brian P. Walenz +A src/stores/tgStoreFilter.C nihh20190715Brian P. Walenz +A src/stores/tgTig.C nihh20190715Brian P. Walenz +A src/stores/tgTig.H nihh20190715Brian P. Walenz +A src/wtdbg/wtdbgConvert.C nihh20190715Brian P. Walenz +A src/overlapAlign/computeAlignments.C nihh20190714Brian P. Walenz +A src/overlapAlign/computeOverlapAlignment.C nihh20190714Brian P. Walenz +A src/overlapAlign/overlapAlign-computation.H nihh20190714Brian P. Walenz +A src/overlapAlign/overlapAlign-globalData.H nihh20190714Brian P. Walenz +A src/overlapAlign/overlapAlign.C nihh20190714Brian P. Walenz +A src/stores/sqCache.C nihh20190714Brian P. Walenz +A src/stores/sqCache.H nihh20190714Brian P. Walenz +A src/stores/sqCache.C nihh20190714Brian P. Walenz +A documentation/source/parameter-reference.rst nihh20190711Sergey Koren +A documentation/source/quick-start.rst nihh20190711Sergey Koren +A src/pipelines/canu.pl nihh20190711Sergey Koren +A src/pipelines/canu/Defaults.pm nihh20190711Sergey Koren +A src/utility/files-buffered-implementation.H nihh20190708Brian P. Walenz +A src/utility/sequence.C nihh20190705Brian P. Walenz +A src/utility/sequence.H nihh20190705Brian P. Walenz +A src/utility/files-buffered.C nihh20190705Brian P. Walenz +A src/utility/files-buffered.H nihh20190705Brian P. Walenz +A src/utility/bits.C nihh20190705Brian P. Walenz +A src/utility/bits.H nihh20190705Brian P. Walenz +A src/utility/arrays.H nihh20190705Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20190628Sergey Koren +A src/overlapInCore/overlapImport.C nihh20190628Sergey Koren +A src/stores/ovOverlap.C nihh20190628Sergey Koren +A src/utility/sampledDistribution.H nihh20190627Brian P. Walenz +A src/sequence/sequence-simulate.C nihh20190627Brian P. Walenz +A src/sequence/sequence.C nihh20190627Brian P. Walenz +A src/pipelines/canu/OverlapInCore.pm nihh20190627Brian P. Walenz +A src/pipelines/canu/OverlapMMap.pm nihh20190627Brian P. Walenz +A src/pipelines/canu/OverlapMhap.pm nihh20190627Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20190627Brian P. Walenz +A src/stores/ovStoreBucketizer.C nihh20190627Brian P. Walenz +A src/overlapAlign/overlapAlign-computation.H nihh20190610Brian P. Walenz +A src/main.mk nihh20190610Brian P. Walenz +A src/fastq-utilities/README nihh20190610Brian P. Walenz +A src/overlapAlign/clearRangeFile.C nihh20190607Brian P. Walenz +A src/overlapAlign/clearRangeFile.H nihh20190607Brian P. Walenz +A src/overlapAlign/overlapAlign-globalData.H nihh20190607Brian P. Walenz +A src/overlapAlign/overlapAlign.C nihh20190607Brian P. Walenz +A src/overlapAlign/overlapAlign.mk nihh20190607Brian P. Walenz +A src/overlapAlign/trimRead.C nihh20190607Brian P. Walenz +A src/stores/sqCache.C nihh20190607Brian P. Walenz +A src/stores/sqCache.H nihh20190607Brian P. Walenz +A src/pipelines/canu.pl nihh20190607Brian P. Walenz +A src/pipelines/canu/Output.pm nihh20190607Brian P. Walenz +A src/stores/ovStoreFile.C nihh20190605Brian P. Walenz +A src/stores/ovStoreFile.H nihh20190605Brian P. Walenz +A documentation/source/parameter-reference.rst nihh20190604Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20190604Brian P. Walenz +A src/pipelines/canu/OverlapMMap.pm nihh20190604Brian P. Walenz +A src/pipelines/canu/OverlapMhap.pm nihh20190604Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20190604Brian P. Walenz +A src/stores/ovStoreFile.C nihh20190603Brian P. Walenz +A src/stores/ovStoreFile.H nihh20190603Brian P. Walenz +A src/stores/ovStoreFile.H nihh20190603Brian P. Walenz +A src/stores/ovStoreBucketizer.C nihh20190603Brian P. Walenz +A src/utility/files.C nihh20190531Brian P. Walenz +A src/utility/files.H nihh20190531Brian P. Walenz +A src/pipelines/canu/Grid_PBSTorque.pm nihh20190531Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20190528Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20190528Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20190528Brian P. Walenz +A src/utility/kmers-exact.C nihh20190528Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20190528Brian P. Walenz +A src/Makefile nihh20190530Brian P. Walenz +A src/sequence/sequence.C nihh20190521Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190521Brian P. Walenz +A src/pipelines/canu.pl nihh20190521Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20190521Brian P. Walenz +A src/sequence/sequence-extract.C nihh20190521Brian P. Walenz +A src/stores/sqLibrary.C nihh20190521Brian P. Walenz +A src/stores/sqLibrary.H nihh20190521Brian P. Walenz +A src/stores/sqStore.C nihh20190521Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190521Brian P. Walenz +A src/utgcns/utgcns.C nihh20190521Brian P. Walenz +A src/stores/sqStoreConstructor.C nihh20190521Brian P. Walenz +A src/utility/files-buffered.C nihh20190520Brian P. Walenz +A src/overlapAlign/overlapAlign.C nihh20190520Brian P. Walenz +A src/overlapAlign/computeOverlapAlignment.C nihh20190520Brian P. Walenz +A src/meryl/meryl-lookup.C nihh20190520Brian P. Walenz +A src/utility/sequence.C nihh20190520Brian P. Walenz +A src/utility/sequence.H nihh20190520Brian P. Walenz +A src/sequence/sequence-extract.C nihh20190520Brian P. Walenz +A src/sequence/sequence-simulate.C nihh20190520Brian P. Walenz +A src/sequence/sequence-extract.C nihh20190520Brian P. Walenz +A src/sequence/sequence.C nihh20190520Brian P. Walenz +A src/sequence/sequence.H nihh20190520Brian P. Walenz +A src/stores/tgStoreLoad.C nihh20190520Brian P. Walenz +A src/stores/tgTig.C nihh20190520Brian P. Walenz +A src/stores/tgTig.H nihh20190520Brian P. Walenz +A src/utility/sampledDistribution.H nihh20190520Brian P. Walenz +A documentation/source/quick-start.rst nihh20190517Brian P. Walenz +A documentation/source/tutorial.rst nihh20190517Brian P. Walenz +A src/pipelines/canu/Consensus.pm nihh20190517Brian P. Walenz +A src/pipelines/canu/Output.pm nihh20190517Brian P. Walenz +A src/pipelines/canu/Unitig.pm nihh20190517Brian P. Walenz +A src/overlapAlign/overlapAlign.C nihh20190517Brian P. Walenz +A src/overlapAlign/computeOverlapAlignment.C nihh20190517Brian P. Walenz +A src/overlapAlign/computeAlignments.C nihh20190516Brian P. Walenz +A src/overlapAlign/computeOverlapAlignment.C nihh20190516Brian P. Walenz +A src/overlapAlign/overlapAlign-computation.H nihh20190516Brian P. Walenz +A src/overlapAlign/overlapAlign.C nihh20190516Brian P. Walenz +A src/stores/ovStore.C nihh20190515Brian P. Walenz +A src/stores/sqStoreDumpMetaData.C nihh20190514Brian P. Walenz +A src/stores/sqStore.C nihh20190514Brian P. Walenz +A src/overlapAlign/computeAlignments.C nihh20190514Brian P. Walenz +A src/overlapAlign/computeOverlapAlignment.C nihh20190514Brian P. Walenz +A src/overlapAlign/overlapAlign-computation.H nihh20190514Brian P. Walenz +A src/overlapAlign/overlapAlign-globalData.H nihh20190514Brian P. Walenz +A src/overlapAlign/overlapAlign.C nihh20190514Brian P. Walenz +A src/overlapAlign/computeAlignments.C nihh20190514Brian P. Walenz +A src/overlapAlign/computeOverlapAlignment.C nihh20190514Brian P. Walenz +A src/overlapAlign/overlapAlign-computation.H nihh20190514Brian P. Walenz +A src/overlapAlign/overlapAlign-globalData.H nihh20190514Brian P. Walenz +A src/overlapAlign/overlapAlign.C nihh20190514Brian P. Walenz +A src/overlapAlign/trimRead.C nihh20190514Brian P. Walenz +A src/meryl/meryl.C nihh20190508Brian P. Walenz +A src/pipelines/canu/Unitig.pm nihh20190508Brian P. Walenz +A src/pipelines/canu/OverlapMMap.pm nihh20190508Brian P. Walenz +A src/pipelines/canu/OverlapMhap.pm nihh20190508Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20190508Brian P. Walenz +A src/overlapAlign/computeAlignments.C nihh20190502Brian P. Walenz +A src/overlapAlign/computeOverlapAlignment.C nihh20190502Brian P. Walenz +A src/overlapAlign/overlapAlign-computation.H nihh20190502Brian P. Walenz +A src/overlapAlign/overlapAlign-globalData.H nihh20190502Brian P. Walenz +A src/overlapAlign/overlapAlign.C nihh20190502Brian P. Walenz +A src/overlapAlign/trimRead.C nihh20190502Brian P. Walenz +A src/stores/ovStore.C nihh20190502Brian P. Walenz +A src/pipelines/canu/Grid_LSF.pm nihh20190502Brian P. Walenz +A src/overlapAlign/computeAlignments.C nihh20190430Brian P. Walenz +A src/overlapAlign/overlapAlign-computation.H nihh20190430Brian P. Walenz +A src/overlapAlign/overlapAlign.C nihh20190429Brian P. Walenz +A src/overlapAlign/computeAlignments.C nihh20190429Brian P. Walenz +A src/overlapAlign/overlapAlign.C nihh20190429Brian P. Walenz +A src/overlapAlign/overlapAlign.mk nihh20190429Brian P. Walenz +A src/overlapAlign/trimRead.C nihh20190429Brian P. Walenz +A src/overlapAlign/overlapAlign-computation.H nihh20190429Brian P. Walenz +A src/overlapAlign/overlapAlign-globalData.H nihh20190429Brian P. Walenz +A src/overlapAlign/overlapAlign.C nihh20190429Brian P. Walenz +A src/utility/sweatShop.C nihh20190429Brian P. Walenz +A src/sequence/sequence-simulate.C nihh20190429Brian P. Walenz +A src/utility/sampledDistribution.H nihh20190429Brian P. Walenz +A src/overlapAlign/computeOverlapAlignment.C nihh20190425Brian P. Walenz +A src/overlapAlign/overlapAlign-computation.H nihh20190425Brian P. Walenz +A src/overlapAlign/overlapAlign-globalData.H nihh20190425Brian P. Walenz +A src/overlapAlign/overlapAlign.C nihh20190425Brian P. Walenz +A src/overlapAlign/computeOverlapAlignment.C nihh20190425Brian P. Walenz +A src/overlapInCore/edalign.C nihh20190425Brian P. Walenz +A src/stores/ovStoreDump.C nihh20190425Brian P. Walenz +A src/main.mk nihh20190422Brian P. Walenz +A src/overlapAlign/alignStats.H nihh20190422Brian P. Walenz +A src/overlapAlign/computeOverlapAlignment.C nihh20190422Brian P. Walenz +A src/overlapAlign/overlapAlign-computation.H nihh20190422Brian P. Walenz +A src/overlapAlign/overlapAlign-globalData.H nihh20190422Brian P. Walenz +A src/overlapAlign/overlapAlign-threadData.H nihh20190422Brian P. Walenz +A src/overlapAlign/overlapAlign.C nihh20190422Brian P. Walenz +A src/overlapAlign/overlapAlign.mk nihh20190422Brian P. Walenz +A src/overlapInCore/edalign.C nihh20190422Brian P. Walenz +A src/utility/edlib.C nihh20190422Brian P. Walenz +A src/utility/edlib.H nihh20190422Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20190420Sergey Koren +A src/sequence/sequence-simulate.C nihh20190419Brian P. Walenz +A src/sequence/sequence.C nihh20190419Brian P. Walenz +A src/Makefile nihh20190418Brian P. Walenz +A src/sequence/sequence-simulate.C nihh20190418Brian P. Walenz +A src/sequence/sequence-summarize.C nihh20190418Brian P. Walenz +A src/sequence/sequence.C nihh20190418Brian P. Walenz +A src/sequence/sequence.H nihh20190418Brian P. Walenz +A src/utility/sampledDistribution.H nihh20190418Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20190417Brian P. Walenz +A src/meryl/meryl-lookup.C nihh20190417Brian P. Walenz +A src/utility/kmers-exact.C nihh20190417Brian P. Walenz +A src/utility/kmers.H nihh20190417Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20190416Brian P. Walenz +A src/pipelines/canu/Grid_LSF.pm nihh20190416Brian P. Walenz +A src/pipelines/canu/Grid_PBSTorque.pm nihh20190416Brian P. 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Walenz +A src/stores/ovStoreBuild.C nihh20190410Brian P. Walenz +A src/stores/ovStoreDump.C nihh20190410Brian P. Walenz +A src/stores/ovStoreSorter.C nihh20190410Brian P. Walenz +A src/stores/ovStoreStats.C nihh20190410Brian P. Walenz +A src/stores/sqStoreConstructor.C nihh20190410Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20190410Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190410Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190410Brian P. Walenz +A src/utility/edlib.C nihh20190410Brian P. Walenz +A src/stores/ovStore.C nihh20190410Brian P. Walenz +A src/Makefile nihh20190401Brian P. Walenz +A src/pipelines/canu-time.pl nihh20190401Brian P. Walenz +A src/stores/sqStoreCreate.C nihh20190329Brian P. Walenz +A src/sequence/sequence.C nihh20190329Brian P. Walenz +A src/correction/falconConsensus.C nihh20190328Brian P. Walenz +A src/correction/falconConsensus.H nihh20190328Brian P. Walenz +A src/correction/falconsense.C nihh20190328Brian P. Walenz +A src/correction/filterCorrectionLayouts.C nihh20190328Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20190328Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20190328Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20190328Brian P. Walenz +A src/stores/sqStoreConstructor.C nihh20190328Brian P. Walenz +A src/utility/system.C nihh20190328Brian P. Walenz +A src/utility/system.H nihh20190328Brian P. Walenz +A src/pipelines/canu/OverlapErrorAdjustment.pm nihh20190328Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20190328Brian P. Walenz +A src/Makefile nihh20190328Brian P. Walenz +A src/utility/kmers-exact.C nihh20190327Brian P. Walenz +A documentation/source/tutorial.rst nihh20190327Sergey Koren +A src/stores/sqRead.H nihh20190325Brian P. Walenz +A src/stores/sqStore.C nihh20190325Brian P. Walenz +A src/stores/sqStoreDumpMetaData.C nihh20190325Brian P. Walenz +A src/stores/sqStorePartition.C nihh20190325Brian P. Walenz +A src/bogart/AS_BAT_MergeOrphans.C nihh20190322Brian P. Walenz +A src/meryl/meryl-import.C nihh20190321Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20190319Brian P. Walenz +A src/pipelines/canu/Grid_DNANexus.pm nihh20190319Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20190319Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20190319Brian P. Walenz +A src/pipelines/canu/Grid_SGE.pm nihh20190319Brian P. Walenz +A src/pipelines/canu/Grid_Slurm.pm nihh20190319Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20190318Brian P. Walenz +A documentation/source/faq.rst nihh20190315Sergey Koren +A src/utgcns/unitigConsensus.C nihh20190314Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190314Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20190312Brian P. Walenz +A src/pipelines/canu.pl nihh20190312Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20190312Brian P. Walenz +A documentation/source/parameter-reference.rst nihh20190312Brian P. Walenz +A documentation/source/tutorial.rst nihh20190312Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20190312Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20190312Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20190312Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190312Brian P. Walenz +A src/utgcns/unitigConsensus.H nihh20190312Brian P. Walenz +A src/bogart/bogart.C nihh20190311Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190311Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190311Brian P. Walenz +A src/dx-canu/src/canu.sh nihh20190308Brian P. Walenz +A src/pipelines/canu/Consensus.pm nihh20190308Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20190308Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20190308Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20190308Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20190308Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20190308Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20190308Brian P. Walenz +A src/pipelines/canu/OverlapInCore.pm nihh20190308Brian P. Walenz +A src/pipelines/canu/OverlapMMap.pm nihh20190308Brian P. Walenz +A src/pipelines/canu/OverlapMhap.pm nihh20190308Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20190308Brian P. Walenz +A src/pipelines/canu/SequenceStore.pm nihh20190308Brian P. Walenz +A src/pipelines/canu/Unitig.pm nihh20190308Brian P. Walenz +A src/pipelines/object-store-simulator.pl nihh20190308Brian P. Walenz +A src/utility/objectStore.C nihh20190308Brian P. Walenz +A src/sequence/sequence.C nihh20190307Brian P. Walenz +A src/meryl/meryl-lookup.C nihh20190301Brian P. Walenz +A src/main.mk nihh20190301Brian P. Walenz +A src/overlapBasedTrimming/mergeRanges.C nihh20190301Brian P. Walenz +A src/overlapBasedTrimming/mergeRanges.mk nihh20190301Brian P. Walenz +A src/stores/loadTrimmedReads.C nihh20190228Brian P. Walenz +A src/utility/strings.C nihh20190228Brian P. Walenz +A src/stores/loadTrimmedReads.C nihh20190228Brian P. Walenz +A src/meryl/meryl-lookup.C nihh20190225Brian P. Walenz +A src/utility/kmers.H nihh20190225Brian P. Walenz +A src/utility/kmers.H nihh20190225Brian P. Walenz +A src/utility/kmers.H nihh20190225Brian P. Walenz +A src/meryl/meryl-lookup.C nihh20190225Arang Rhie +A src/meryl/meryl.C nihh20190225Brian P. Walenz +A src/meryl/merylOp-count.C nihh20190223Brian P. Walenz +A src/utility/files-buffered-implementation.H nihh20190223Brian P. Walenz +A src/utility/files-buffered.C nihh20190223Brian P. Walenz +A src/utility/files-buffered.H nihh20190223Brian P. Walenz +A src/utility/sequence.C nihh20190223Brian P. Walenz +A src/meryl/merylOp-count.C nihh20190222Brian P. Walenz +A src/Makefile nihh20190221Brian P. Walenz +A src/meryl/meryl.C nihh20190220Brian P. Walenz +A src/meryl/merylCountArray.C nihh20190220Brian P. Walenz +A src/canu_version_update.pl nihh20190219Brian P. Walenz +A src/utility/stddev.H nihh20190219Brian P. Walenz +A src/utility/stddevTest.C nihh20190219Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20190216Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20190215Brian P. Walenz +A src/pipelines/canu/Grid_SGE.pm nihh20190215Brian P. Walenz +A src/meryl/meryl-import.C nihh20190214Brian P. Walenz +A src/meryl/meryl-lookup.C nihh20190214Brian P. Walenz +A src/meryl/merylCountArray.C nihh20190214Brian P. Walenz +A src/meryl/merylCountArray.H nihh20190214Brian P. Walenz +A src/meryl/merylInput.C nihh20190214Brian P. Walenz +A src/meryl/merylInput.H nihh20190214Brian P. Walenz +A src/meryl/merylOp-count.C nihh20190214Brian P. Walenz +A src/meryl/merylOp-histogram.C nihh20190214Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20190214Brian P. Walenz +A src/meryl/merylOp.C nihh20190214Brian P. Walenz +A src/meryl/merylOp.H nihh20190214Brian P. Walenz +A src/utility/kmers-exact.C nihh20190214Brian P. Walenz +A src/utility/kmers-reader.C nihh20190214Brian P. Walenz +A src/utility/kmers-statistics.C nihh20190214Brian P. Walenz +A src/utility/kmers-writer-block.C nihh20190214Brian P. Walenz +A src/utility/kmers-writer-block.H nihh20190214Brian P. Walenz +A src/utility/kmers-writer-stream.C nihh20190214Brian P. Walenz +A src/utility/kmers-writer-stream.H nihh20190214Brian P. Walenz +A src/utility/kmers-writer.C nihh20190214Brian P. Walenz +A src/utility/kmers.H nihh20190214Brian P. Walenz +A src/meryl/meryl-import.C nihh20190212Brian P. Walenz +A src/meryl/merylOp-histogram.C nihh20190212Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20190212Brian P. Walenz +A src/utility/kmers-exact.C nihh20190212Brian P. Walenz +A src/utility/kmers-statistics.C nihh20190212Brian P. Walenz +A src/utility/kmers.H nihh20190212Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20190212Brian P. Walenz +A src/correction/falconsense.C nihh20190212Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20190212Brian P. Walenz +A src/main.mk nihh20190212Brian P. Walenz +A src/stores/sqCache.C nihh20190212Brian P. Walenz +A src/stores/sqCache.H nihh20190212Brian P. Walenz +A src/stores/sqRead.H nihh20190212Brian P. Walenz +A src/stores/sqStore.C nihh20190212Brian P. Walenz +A src/stores/sqStore.H nihh20190212Brian P. Walenz +A src/stores/sqStoreEncode.C nihh20190212Brian P. Walenz +A src/stores/sqRead.H nihh20190212Brian P. Walenz +A addCopyrights.dat nihh20190207Brian P. Walenz +A src/main.mk nihh20190207Brian P. Walenz +A src/main.mk nihh20190207Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190207Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190131Brian P. Walenz +A src/main.mk nihh20190129Brian P. Walenz +A src/utility/stddevTest.C nihh20190129Brian P. Walenz +A src/utility/stddevTest.mk nihh20190129Brian P. Walenz +A src/utility/stddev.H nihh20190129Brian P. Walenz +A src/pipelines/canu/OverlapMhap.pm nihh20190124Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20190124Brian P. Walenz +A src/meryl/meryl.C nihh20190117Brian P. Walenz +A src/stores/tgTig.C nihh20190117Brian P. Walenz +A src/stores/tgTig.H nihh20190117Brian P. Walenz +A src/stores/tgTigMultiAlignDisplay.C nihh20190117Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190117Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190117Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190117Brian P. Walenz +A src/utility/bits.C nihh20190117Brian P. Walenz +A src/utility/bits.H nihh20190117Brian P. Walenz +A documentation/source/parameter-reference.rst nihh20190111Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20190111Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20190111Brian P. Walenz +A src/pipelines/canu/Grid_DNANexus.pm nihh20190111Brian P. Walenz +A src/pipelines/canu/Grid_LSF.pm nihh20190111Brian P. Walenz +A src/pipelines/canu/Grid_PBSTorque.pm nihh20190111Brian P. Walenz +A src/pipelines/canu/Grid_SGE.pm nihh20190111Brian P. Walenz +A src/pipelines/canu/Grid_Slurm.pm nihh20190111Brian P. Walenz +A src/overlapInCore/libedlib/edlib.C nihh20190110Brian P. Walenz +A src/sequence/sequence-mutate.C nihh20190109Brian P. Walenz +A src/sequence/sequence.C nihh20190109Brian P. Walenz +A src/sequence/sequence.H nihh20190109Brian P. Walenz +A src/sequence/sequence.mk nihh20190109Brian P. Walenz +A addCopyrights.dat nihh20190103Brian P. Walenz +A src/sequence/sequence-extract.C nihh20190103Brian P. Walenz +A src/sequence/sequence-generate.C nihh20190103Brian P. Walenz +A src/sequence/sequence-sample.C nihh20190103Brian P. Walenz +A src/sequence/sequence-shiftregister.C nihh20190103Brian P. Walenz +A src/sequence/sequence-simulate.C nihh20190103Brian P. Walenz +A src/sequence/sequence-summarize.C nihh20190103Brian P. Walenz +A src/sequence/sequence.C nihh20190103Brian P. Walenz +A src/sequence/sequence.H nihh20190103Brian P. Walenz +A src/sequence/sequence-extract.C nihh20190103Brian P. Walenz +A src/sequence/sequence-generate.C nihh20190103Brian P. Walenz +A src/sequence/sequence-sample.C nihh20190103Brian P. Walenz +A src/sequence/sequence-shiftregister.C nihh20190103Brian P. Walenz +A src/sequence/sequence-simulate.C nihh20190103Brian P. Walenz +A src/sequence/sequence-summarize.C nihh20190103Brian P. Walenz +A src/sequence/sequence.C nihh20190103Brian P. Walenz +A src/sequence/sequence.H nihh20190103Brian P. Walenz +A src/sequence/sequence.mk nihh20190103Brian P. Walenz +A src/bogart/AS_BAT_OptimizePositions.C nihh20190102Brian P. Walenz +A src/bogart/AS_BAT_PlaceReadUsingOverlaps.C nihh20190102Brian P. Walenz +A src/bogart/AS_BAT_PlaceReadUsingOverlaps.H nihh20190102Brian P. Walenz +A src/bogart/AS_BAT_Unitig_AddRead.C nihh20190102Brian P. Walenz +A src/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C nihh20190102Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20190102Brian P. Walenz +A src/stores/loadErates.C nihh20190102Brian P. Walenz +A src/stores/ovStoreFilter.C nihh20190102Brian P. Walenz +A src/stores/ovStoreWriter.C nihh20190102Brian P. Walenz +A src/stores/sqLibrary.C nihh20190102Brian P. Walenz +A src/stores/sqLibrary.H nihh20190102Brian P. Walenz +A src/stores/sqRead.H nihh20190102Brian P. Walenz +A src/stores/sqStoreConstructor.C nihh20190102Brian P. Walenz +A src/stores/sqStoreCreate.C nihh20190102Brian P. Walenz +A src/stores/sqStoreDumpFASTQ.C nihh20190102Brian P. Walenz +A src/stores/sqStoreInfo.C nihh20190102Brian P. Walenz +A src/stores/sqStorePartition.C nihh20190102Brian P. Walenz +A src/stores/tgStoreCompress.C nihh20190102Brian P. Walenz +A src/utgcns/unitigConsensus.H nihh20190102Brian P. Walenz +A src/utility/files-compressed.C nihh20190102Brian P. Walenz +A src/utility/files-compressed.H nihh20190102Brian P. Walenz +A src/utility/speedCounter.H nihh20190102Brian P. Walenz +A src/sequence/sequence.C nihh20190102Brian P. Walenz +A addCopyrights.pl nihh20190102Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20190102Brian P. Walenz +A src/stores/sqStoreCreate.C nihh20190102Brian P. Walenz +A src/stores/sqStoreCreate.C nihh20190102Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20190102Brian P. Walenz +A documentation/source/faq.rst nihh20181220Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20181220Brian P. Walenz +A src/meryl/meryl.C nihh20181220Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20181220Brian P. Walenz +A src/meryl/merylOp.H nihh20181220Brian P. Walenz +A src/utility/kmers-reader.C nihh20181220Brian P. Walenz +A src/utility/kmers.H nihh20181220Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20181220Brian P. Walenz +A src/meryl/merylOp.H nihh20181220Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20181220Brian P. Walenz +A src/meryl/merylOp.H nihh20181220Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20181220Brian P. Walenz +A src/utility/kmers-writer-stream.C nihh20181220Brian P. Walenz +A src/utility/kmers.H nihh20181220Brian P. Walenz +A src/meryl/meryl.C nihh20181219Brian P. Walenz +A src/sequence/sequence.C nihh20181217Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20181217Brian P. Walenz +A src/utgcns/utgcns.C nihh20181217Brian P. Walenz +A src/utgcns/utgcns.C nihh20181217Brian P. Walenz +A documentation/source/faq.rst nihh20181216Sergey Koren +A documentation/source/faq.rst nihh20181216Sergey Koren +A src/sequence/sequence.C nihh20181212Brian P. Walenz +A src/Makefile nihh20181211Brian P. Walenz +A src/stores/ovStoreFile.C nihh20181211Brian P. Walenz +A README.md nihh20181211Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20181210Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20181210Brian P. Walenz +A src/bogart/AS_BAT_OptimizePositions.C nihh20181210Brian P. Walenz +A src/stores/tgStoreDump.C nihh20181210Brian P. Walenz +A src/pipelines/canu.pl nihh20181207Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20181204Brian P. Walenz +A src/utgcns/unitigConsensus.H nihh20181204Brian P. Walenz +A src/utgcns/utgcns.C nihh20181204Brian P. Walenz +A src/pipelines/canu/Grid_Slurm.pm nihh20181204Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20181204Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20181204Brian P. Walenz +A src/stores/tgStoreDump.C nihh20181203Brian P. Walenz +A src/utility/bits.H nihh20181203Brian P. Walenz +A src/Makefile nihh20181203Brian P. Walenz +A src/utgcns/unitigConsensus.C nihh20181115Brian P. Walenz +A src/utgcns/unitigConsensus.H nihh20181115Brian P. Walenz +A addCopyrights.dat nihh20181115Brian P. Walenz +A src/main.mk nihh20181115Brian P. Walenz +A src/utgcns/utgcns.mk nihh20181115Brian P. Walenz +A src/main.mk nihh20181115Brian P. Walenz +A src/utgcns/libcns/unitigConsensus.C nihh20181115Brian P. Walenz +A src/utgcns/libcns/unitigConsensus.H nihh20181115Brian P. Walenz +A src/utgcns/utgcns.C nihh20181115Brian P. Walenz +A src/utgcns/utgcns.mk nihh20181115Brian P. Walenz +A src/utgcns/libcns/unitigConsensus.C nihh20181115Brian P. Walenz +A src/stores/ovStoreBuild.C nihh20181115Brian P. Walenz +A src/stores/ovStoreConfig.C nihh20181115Brian P. Walenz +A src/meryl/merylCountArray.C nihh20181110Brian P. Walenz +A src/utgcns/libcns/unitigConsensus.C nihh20181109Brian P. Walenz +A src/correction/falconsense.C nihh20181109Brian P. Walenz +A src/stores/tgTig.C nihh20181109Brian P. Walenz +A src/stores/tgTig.H nihh20181109Brian P. Walenz +A src/utgcns/utgcns.C nihh20181109Brian P. Walenz +A src/main.mk nihh20181107Brian P. Walenz +A src/utility/filesTest.C nihh20181107Brian P. Walenz +A src/utility/filesTest.mk nihh20181107Brian P. Walenz +A src/utility/bitsTest.C nihh20181107Brian P. Walenz +A src/pipelines/canu/Consensus.pm nihh20181107Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20181107Brian P. Walenz +A src/pipelines/canu.pl nihh20181107Brian P. Walenz +A documentation/source/parameter-reference.rst nihh20181107Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20181107Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20181107Brian P. Walenz +A src/pipelines/canu/OverlapBasedTrimming.pm nihh20181107Brian P. Walenz +A src/pipelines/canu/Unitig.pm nihh20181106Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20181106Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20181106Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20181106Brian P. Walenz +A src/pipelines/canu/Consensus.pm nihh20181106Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20181106Brian P. Walenz +A documentation/source/parameter-reference.rst nihh20181105Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20181105Brian P. Walenz +A src/pipelines/canu/OverlapMMap.pm nihh20181105Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20181105Brian P. Walenz +A src/meryl/merylOp-count.C nihh20181105Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20181105Brian P. Walenz +A src/meryl/merylInput.C nihh20181104Brian P. Walenz +A src/meryl/merylInput.H nihh20181104Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20181104Brian P. Walenz +A src/meryl/merylOp.C nihh20181104Brian P. Walenz +A src/meryl/merylOp.H nihh20181104Brian P. Walenz +A src/utility/kmers-writer.C nihh20181104Brian P. Walenz +A src/utility/kmers.H nihh20181104Brian P. Walenz +A src/main.mk nihh20181102Brian P. Walenz +A src/meryl/meryl-import.C nihh20181102Brian P. Walenz +A src/meryl/meryl-import.mk nihh20181102Brian P. Walenz +A src/meryl/merylCountArray.C nihh20181102Brian P. Walenz +A src/meryl/merylCountArray.H nihh20181102Brian P. Walenz +A src/meryl/merylOp-count.C nihh20181102Brian P. Walenz +A src/meryl/merylCountArray.C nihh20181102Brian P. Walenz +A src/meryl/merylCountArray.H nihh20181102Brian P. Walenz +A src/main.mk nihh20181101Brian P. Walenz +A src/utility/bits.C nihh20181101Brian P. Walenz +A src/utility/bits.H nihh20181101Brian P. Walenz +A src/utility/bitsTest.C nihh20181101Brian P. Walenz +A src/utility/bitsTest.mk nihh20181101Brian P. Walenz +A src/meryl/merylOp-count.C nihh20181030Brian P. Walenz +A src/utility/bits.C nihh20181030Brian P. Walenz +A src/utility/bits.H nihh20181030Brian P. Walenz +A src/utility/bitsTest.C nihh20181030Brian P. Walenz +A src/utility/kmers-exact.C nihh20181030Brian P. Walenz +A src/utility/bits.C nihh20181030Brian P. Walenz +A src/utility/bits.H nihh20181030Brian P. Walenz +A src/utility/bits.H nihh20181030Brian P. Walenz +A src/meryl/merylCountArray.C nihh20181029Brian P. Walenz +A src/meryl/merylCountArray.H nihh20181029Brian P. Walenz +A src/utility/kmers-reader.C nihh20181026Brian P. Walenz +A src/utility/kmers-writer.C nihh20181026Brian P. Walenz +A src/utility/kmers.H nihh20181026Brian P. Walenz +A documentation/source/faq.rst nihh20181026Sergey Koren +A src/pipelines/canu/Grid_LSF.pm nihh20181026Sergey Koren +A src/main.mk nihh20181026Brian P. Walenz +A src/meryl/meryl-lookup.C nihh20181026Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20181026Brian P. Walenz +A src/meryl/merylOp-count.C nihh20181026Brian P. Walenz +A src/meryl/merylOp-countSimple.C nihh20181026Brian P. Walenz +A src/utility/kmers.H nihh20181026Brian P. Walenz +A buildRelease.sh nihh20181025Sergey Koren +A statifyOSX.py nihh20181025Sergey Koren +A documentation/source/parameter-reference.rst nihh20181025Sergey Koren +A documentation/source/parameter-reference.rst nihh20181025Sergey Koren +A documentation/source/faq.rst nihh20181025Sergey Koren +A documentation/source/tutorial.rst nihh20181025Sergey Koren +A documentation/source/quick-start.rst nihh20181024Sergey Koren +A documentation/source/quick-start.rst nihh20181024Sergey Koren +A documentation/source/quick-start.rst nihh20181024Sergey Koren +A documentation/source/conf.py nihh20181022Brian P. Walenz +A src/canu_version_update.pl nihh20181022Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20181022Brian P. Walenz +A addCopyrights-BuildData.pl nihh20181022Brian P. Walenz +A addCopyrights.dat nihh20181022Brian P. Walenz