diff --git a/addCopyrights-BuildData.pl b/addCopyrights-BuildData.pl index f37396be9..1b8638abf 100644 --- a/addCopyrights-BuildData.pl +++ b/addCopyrights-BuildData.pl @@ -36,6 +36,7 @@ $stoppingCommits{"64459fe33f97f6d23fe036ba1395743d0cdd03e4"} = 1; # 17 APR 2017 $stoppingCommits{"9e9bd674b705f89817b07ff30067210c2d180f42"} = 1; # 14 AUG 2017 $stoppingCommits{"0fff8a511fd7d74081d94ff9e0f6c0351650ae2e"} = 1; # 27 FEB 2018 - v1.7 +$stoppingCommits{"fcc3fe19eb635abd735486d215fbf65c56bcf4ee"} = 1; # 22 OCT 2018 - v1.8 open(F, "< logs") or die "Failed to open 'logs': $!\n"; diff --git a/addCopyrights.dat b/addCopyrights.dat index b30985db5..6b0954e76 100644 --- a/addCopyrights.dat +++ b/addCopyrights.dat @@ -8471,6 +8471,7 @@ A src/AS_UTL/bitPackedFile.C craa20030220Brian P. Walenz A src/AS_UTL/bitPackedFile.C craa20030131Brian P. Walenz A src/AS_UTL/bitPackedFile.C craa20030102Brian P. Walenz D src/AS_UTL/bitPackedFile.C kmer/libutil/bitPackedFile.C +D src/AS_UTL/speedCounter.H kmer/libutil/speedCounter.H A src/AS_UTL/speedCounter.H bnbi20141208Brian P. Walenz A src/AS_UTL/speedCounter.H bnbi20141205Brian P. Walenz A src/AS_UTL/speedCounter.H jcvi20140411Brian P. Walenz @@ -8480,7 +8481,6 @@ A src/AS_UTL/speedCounter.H jcvi20061012Brian P. Walenz A src/AS_UTL/speedCounter.H jcvi20050712Brian P. Walenz A src/AS_UTL/speedCounter.H craa20030506Brian P. Walenz A src/AS_UTL/speedCounter.H craa20030102Brian P. Walenz -D src/AS_UTL/speedCounter.H kmer/libutil/speedCounter.H A src/AS_UTL/bitEncodings.H bnbi20141208Brian P. Walenz A src/AS_UTL/memoryMappedFile.H bnbi20150421Brian P. Walenz A src/AS_UTL/memoryMappedFile.H bnbi20150306Brian P. Walenz @@ -13906,3 +13906,1546 @@ D src/utility/system.H src/utility/timeAndSize.H D src/sequence.H src/utility/AS_UTL_reverseComplement.H D src/sequence.C src/utility/AS_UTL_reverseComplement.C D src/utility/system-stackTrace.C src/utility/AS_UTL_stackTrace.C +A src/pipelines/canu/Configure.pm nihh20181021Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20181021Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20181021Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20181021Brian P. Walenz +A src/utility/kmers-writer.C nihh20181021Brian P. Walenz +A src/meryl/merylOp-count.C nihh20181021Brian P. Walenz +A src/meryl/meryl.C nihh20181021Brian P. Walenz +A src/meryl/merylOp.C nihh20181021Brian P. Walenz +A src/meryl/merylOp.H nihh20181021Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20181020Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20181019Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20181019Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20181019Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20181019Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20181019Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20181019Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20181019Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20181018Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20181018Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20181018Brian P. Walenz +A src/utility/files.C nihh20181018Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20181017Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20181017Brian P. Walenz +A src/utility/files.H nihh20181017Brian P. Walenz +A src/stores/sqRead.H nihh20181017Brian P. Walenz +A src/utgcns/utgcns.C nihh20181017Brian P. Walenz +A src/pipelines/canu.pl nihh20181016Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20181016Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20181016Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20181016Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20181016Brian P. Walenz +A src/dx-canu/src/canu.sh nihh20181016Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20181016Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20181016Brian P. Walenz +A src/pipelines/canu/SequenceStore.pm nihh20181016Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20181016Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20181015Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20181015Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20181015Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20181015Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20181015Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20181015Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20181011Brian P. Walenz +A src/meryl/meryl.C nihh20181011Brian P. Walenz +A src/meryl/merylOp.C nihh20181011Brian P. Walenz +A src/meryl/merylOp.H nihh20181011Brian P. Walenz +A src/meryl/meryl.C nihh20181011Brian P. Walenz +A src/canu_version_update.pl nihh20181011Sergey Koren +A src/meryl/lookup.mk nihh20181011Brian P. Walenz +A src/meryl/meryl.C nihh20181011Brian P. Walenz +A src/meryl/meryl.mk nihh20181011Brian P. Walenz +A src/meryl/merylInput.C nihh20181011Brian P. Walenz +A src/meryl/merylInput.H nihh20181011Brian P. Walenz +A src/meryl/merylOp-count.C nihh20181011Brian P. Walenz +A src/meryl/merylOp.C nihh20181011Brian P. Walenz +A src/meryl/merylOp.H nihh20181011Brian P. Walenz +A src/sequence/sequence.mk nihh20181011Brian P. Walenz +A src/meryl/meryl.C nihh20181011Brian P. Walenz +A src/sequence/sequence.C nihh20181011Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20181011Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20181005Brian P. Walenz +A src/pipelines/canu.pl nihh20181005Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20181005Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20181005Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20181005Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20181005Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20181005Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20181005Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20181003Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20181003Brian P. Walenz +A src/pipelines/canu/OverlapInCore.pm nihh20181003Brian P. Walenz +A src/pipelines/canu/OverlapMMap.pm nihh20181003Brian P. Walenz +A src/pipelines/canu/OverlapMhap.pm nihh20181003Brian P. Walenz +A src/pipelines/object-store-simulator.pl nihh20181003Brian P. Walenz +A src/pipelines/object-store-simulator.pl nihh20181003Brian P. Walenz +A src/pipelines/object-store-simulator.pl nihh20181003Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20181003Brian P. Walenz +A src/pipelines/object-store-simulator.pl nihh20181003Brian P. Walenz +A src/utility/objectStore.C nihh20181003Brian P. Walenz +A src/meryl/meryl.C nihh20181002Brian P. Walenz +A src/meryl/merylOp-histogram.C nihh20181002Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20181002Brian P. Walenz +A src/meryl/merylOp.H nihh20181002Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20181002Brian P. Walenz +A src/pipelines/canu.pl nihh20180928Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180928Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20180928Brian P. Walenz +A src/stores/ovStoreBucketizer.C nihh20180928Brian P. Walenz +A src/stores/ovStoreSorter.C nihh20180928Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20180928Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180928Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180928Brian P. Walenz +A documentation/source/parameter-reference.rst nihh20180928Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180928Brian P. Walenz +A src/pipelines/canu/SequenceStore.pm nihh20180928Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180928Brian P. Walenz +A src/pipelines/object-store-simulator.pl nihh20180928Brian P. Walenz +A documentation/source/parameter-reference.rst nihh20180927Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180927Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180927Brian P. Walenz +A src/pipelines/canu/SequenceStore.pm nihh20180927Brian P. Walenz +A src/Makefile nihh20180927Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180927Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20180927Brian P. Walenz +A src/utility/kmers-exact.C nihh20180927Brian P. Walenz +A src/utility/kmers.H nihh20180927Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20180927Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20180927Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20180927Brian P. Walenz +A src/utility/bits.H nihh20180927Brian P. Walenz +A src/utility/sweatShop.C nihh20180927Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20180926Brian P. Walenz +A src/Makefile nihh20180926Brian P. Walenz +A src/main.mk nihh20180926Brian P. Walenz +A src/main.mk nihh20180926Brian P. Walenz +A src/utility/kmers-exact.C nihh20180925Brian P. Walenz +A src/utility/kmers.H nihh20180925Brian P. Walenz +A src/stores/ovStoreFile.C nihh20180925Brian P. Walenz +A src/stores/ovStoreFile.H nihh20180925Brian P. Walenz +A src/utility/objectStore.C nihh20180925Brian P. Walenz +A src/utility/objectStore.H nihh20180925Brian P. Walenz +A src/pipelines/canu.pl nihh20180924Brian P. Walenz +A src/meryl/meryl.C nihh20180924Brian P. Walenz +A src/utility/kmers-exact.C nihh20180924Brian P. Walenz +A src/pipelines/canu/Consensus.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/ErrorEstimate.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/Output.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/OverlapBasedTrimming.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/OverlapErrorAdjustment.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/OverlapInCore.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/OverlapMMap.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/OverlapMhap.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/SequenceStore.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/Unitig.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20180921Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180921Brian P. Walenz +A src/meryl/merylCountArray.H nihh20180921Brian P. Walenz +A src/meryl/merylCountArray.C nihh20180920Brian P. Walenz +A src/meryl/merylCountArray.H nihh20180920Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180920Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180920Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180920Brian P. Walenz +A src/meryl/meryl.C nihh20180920Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180920Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20180920Brian P. Walenz +A src/utility/files.C nihh20180920Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20180918Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20180918Brian P. Walenz +A src/utgcns/utgcns.C nihh20180917Brian P. Walenz +A src/main.mk nihh20180917Brian P. Walenz +A src/overlapInCore/edalign.mk nihh20180917Brian P. Walenz +A src/overlapInCore/overlapPair.mk nihh20180917Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20180917Brian P. Walenz +A src/pipelines/canu.pl nihh20180917Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180917Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180917Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20180917Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180917Brian P. Walenz +A src/utility/kmers-exact.C nihh20180917Brian P. Walenz +A src/utility/sequence.H nihh20180917Brian P. Walenz +A src/meryl/lookup.C nihh20180913Brian P. Walenz +A src/meryl/lookup.mk nihh20180913Brian P. Walenz +A src/utility/kmers-exact.C nihh20180913Brian P. Walenz +A src/utility/kmers.H nihh20180913Brian P. Walenz +A src/utility/kmers.H nihh20180913Brian P. Walenz +A src/utility/kmers.H nihh20180913Brian P. Walenz +A src/correction/falconsense.C nihh20180910Sergey Koren +A documentation/source/faq.rst nihh20180906Sergey Koren +A src/pipelines/canu/Meryl.pm nihh20180905Brian P. Walenz +A src/pipelines/canu.pl nihh20180905Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20180905Brian P. Walenz +A src/pipelines/canu/Consensus.pm nihh20180905Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180905Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180905Brian P. Walenz +A src/pipelines/canu/OverlapInCore.pm nihh20180905Brian P. Walenz +A src/pipelines/canu/OverlapMhap.pm nihh20180905Brian P. Walenz +A src/pipelines/canu/Unitig.pm nihh20180905Brian P. Walenz +A src/pipelines/trioCanu.pl nihh20180905Brian P. Walenz +A src/meryl/meryl.C nihh20180904Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20180904Brian P. Walenz +A src/meryl/merylOp.C nihh20180904Brian P. Walenz +A src/meryl/merylOp.H nihh20180904Brian P. Walenz +A src/meryl/merylInput.C nihh20180904Brian P. Walenz +A src/meryl/merylOp-histogram.C nihh20180904Brian P. Walenz +A src/Makefile nihh20180904Brian P. Walenz +A src/utility/kmers.H nihh20180904Brian P. Walenz +A src/utility/kmers-reader.C nihh20180904Brian P. Walenz +A src/utility/kmers.H nihh20180904Brian P. Walenz +A src/utility/bits.H nihh20180904Brian P. Walenz +A src/utility/system.C nihh20180904Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180828Brian P. Walenz +A src/meryl/merylOp-countSimple.C nihh20180828Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20180828Brian P. Walenz +A src/meryl/merylOp.H nihh20180828Brian P. Walenz +A src/meryl/findSeedThreshold.C nihh20180827Brian P. Walenz +A src/utility/kmers-exact.C nihh20180827Brian P. Walenz +A src/meryl/meryl.C nihh20180825Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20180825Brian P. Walenz +A src/pipelines/canu.pl nihh20180825Brian P. Walenz +A src/main.mk nihh20180825Brian P. Walenz +A src/meryl/meryl.C nihh20180825Brian P. Walenz +A src/meryl/merylCountArray.C nihh20180825Brian P. Walenz +A src/meryl/merylCountArray.H nihh20180825Brian P. Walenz +A src/meryl/merylInput.C nihh20180825Brian P. Walenz +A src/meryl/merylInput.H nihh20180825Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180825Brian P. Walenz +A src/meryl/merylOp-countSimple.C nihh20180825Brian P. Walenz +A src/meryl/merylOp-histogram.C nihh20180825Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20180825Brian P. Walenz +A src/meryl/merylOp.C nihh20180825Brian P. Walenz +A src/meryl/merylOp.H nihh20180825Brian P. Walenz +A src/utility/kmers-reader.C nihh20180825Brian P. Walenz +A src/utility/kmers-writer-block.C nihh20180825Brian P. Walenz +A src/utility/kmers-writer-block.H nihh20180825Brian P. Walenz +A src/utility/kmers-writer-stream.C nihh20180825Brian P. Walenz +A src/utility/kmers-writer-stream.H nihh20180825Brian P. Walenz +A src/utility/kmers-writer.C nihh20180825Brian P. Walenz +A src/utility/kmers.C nihh20180825Brian P. Walenz +A src/utility/kmers.H nihh20180825Brian P. Walenz +A src/utility/files.C nihh20180823Brian P. Walenz +A src/utility/kmers.H nihh20180821Brian P. Walenz +A src/utility/kmers-exact.C nihh20180821Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20180821Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20180821Brian P. Walenz +A src/utility/kmers-writer.C nihh20180821Brian P. Walenz +A src/utility/kmers-writer.C nihh20180821Brian P. Walenz +A src/utility/bits.H nihh20180821Brian P. Walenz +A src/utility/kmers.H nihh20180821Brian P. Walenz +A src/utility/kmers.H nihh20180821Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180816Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180816Brian P. Walenz +A src/meryl/merylOp-countSimple.C nihh20180816Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180816Brian P. Walenz +A src/meryl/merylOp-countSimple.C nihh20180816Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20180816Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180816Brian P. Walenz +A src/meryl/merylOp-countSimple.C nihh20180816Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180816Brian P. Walenz +A src/meryl/merylOp-countSimple.C nihh20180816Brian P. Walenz +A src/utility/strings.C nihh20180816Brian P. Walenz +A src/utility/strings.H nihh20180816Brian P. Walenz +A src/meryl/merylInput.C nihh20180815Brian P. Walenz +A src/meryl/meryl.C nihh20180815Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180815Brian P. Walenz +A src/meryl/merylOp-countSimple.C nihh20180815Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20180815Brian P. Walenz +A src/meryl/merylOp.C nihh20180815Brian P. Walenz +A src/meryl/merylOp.H nihh20180815Brian P. Walenz +A src/meryl/merylCountArray.C nihh20180815Brian P. Walenz +A src/meryl/merylCountArray.H nihh20180815Brian P. Walenz +A src/utility/kmers-writer.C nihh20180815Brian P. Walenz +A src/utility/system.C nihh20180815Brian P. Walenz +A src/utility/system.H nihh20180815Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180813Brian P. Walenz +A src/utility/strings.C nihh20180813Brian P. Walenz +A src/utility/strings.H nihh20180813Brian P. Walenz +A src/pipelines/canu.pl nihh20180830Sergey Koren +A src/utgcns/libpbutgcns/AlnGraphBoost.C nihh20180830Sergey Koren +A src/utgcns/libpbutgcns/AlnGraphBoost.H nihh20180830Sergey Koren +A src/utility/sequence.C nihh20180830Sergey Koren +A src/stores/ovStoreFile.C nihh20180828Brian P. Walenz +A src/Makefile nihh20180828Brian P. Walenz +A documentation/source/tutorial.rst nihh20180824Sergey Koren +A documentation/source/tutorial.rst nihh20180824Sergey Koren +A documentation/source/faq.rst nihh20180824Sergey Koren +A documentation/source/faq.rst nihh20180824Sergey Koren +A documentation/source/faq.rst nihh20180820Sergey Koren +A src/utility/files-buffered.C nihh20180813Brian P. Walenz +A src/overlapInCore/overlapImport.C nihh20180813Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180813Brian P. Walenz +A src/bogart/AS_BAT_CreateUnitigs.C nihh20180813Brian P. Walenz +A src/bogart/AS_BAT_OverlapCache.C nihh20180813Brian P. Walenz +A src/bogart/AS_BAT_OverlapCache.C nihh20180813Brian P. Walenz +A src/overlapInCore/liboverlap/prefixEditDistance.C nihh20180810Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180810Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180810Brian P. Walenz +A src/utility/kmers-exact.C nihh20180810Brian P. Walenz +A src/stores/sqStoreEncode.C nihh20180810Brian P. Walenz +A src/meryl/merylInput.C nihh20180810Brian P. Walenz +A src/meryl/merylInput.H nihh20180810Brian P. Walenz +A src/utility/bits.C nihh20180810Brian P. Walenz +A src/utility/bits.H nihh20180810Brian P. Walenz +A src/stores/ovStoreDump.C nihh20180810Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180810Brian P. Walenz +A src/stores/ovOverlap.C nihh20180810Brian P. Walenz +A src/sequence/sequence.C nihh20180810Brian P. Walenz +A src/overlapBasedTrimming/clearRangeFile.H nihh20180810Brian P. Walenz +A src/mhap/mhapConvert.C nihh20180810Brian P. Walenz +A src/minimap/mmapConvert.C nihh20180810Brian P. Walenz +A src/stores/ovStoreIndexer.C nihh20180810Brian P. Walenz +A src/stores/ovStoreStats.C nihh20180810Brian P. Walenz +A src/stores/sqStore.C nihh20180810Brian P. Walenz +A src/utility/arrays.H nihh20180810Brian P. Walenz +A src/utility/arrays.H nihh20180810Brian P. Walenz +A src/utility/arrays.H nihh20180810Brian P. Walenz +A src/stores/sqStoreBlobWriter.H nihh20180810Brian P. Walenz +A src/stores/sqStoreCreate.C nihh20180810Brian P. Walenz +A src/utility/kmers-exact.C nihh20180810Brian P. Walenz +A src/bogart/AS_BAT_OverlapCache.C nihh20180810Brian P. Walenz +A src/correction/filterCorrectionOverlaps.C nihh20180810Brian P. Walenz +A src/correction/generateCorrectionLayouts.C nihh20180810Brian P. Walenz +A src/merTrim/merTrimResult.H nihh20180810Brian P. Walenz +A src/meryl-san/libleaff/sffFile.C nihh20180810Brian P. Walenz +A src/overlapBasedTrimming/clearRangeFile.H nihh20180810Brian P. Walenz +A src/overlapBasedTrimming/splitReads.C nihh20180810Brian P. Walenz +A src/overlapErrorAdjustment/analyzeAlignment.C nihh20180810Brian P. Walenz +A src/overlapErrorAdjustment/correctOverlaps.C nihh20180810Brian P. Walenz +A src/overlapErrorAdjustment/findErrors-Output.C nihh20180810Brian P. Walenz +A src/stores/loadErates.C nihh20180810Brian P. Walenz +A src/stores/ovStore.H nihh20180810Brian P. Walenz +A src/stores/ovStoreConfig.H nihh20180810Brian P. Walenz +A src/stores/ovStoreFile.C nihh20180810Brian P. Walenz +A src/stores/ovStoreFile.H nihh20180810Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180810Brian P. Walenz +A src/stores/sqStore.C nihh20180810Brian P. Walenz +A src/stores/sqStoreConstructor.C nihh20180810Brian P. Walenz +A src/stores/sqStorePartition.C nihh20180810Brian P. Walenz +A src/stores/tgStore.C nihh20180810Brian P. Walenz +A src/stores/tgTig.C nihh20180810Brian P. Walenz +A src/utility/bits.C nihh20180810Brian P. Walenz +A src/utility/files-buffered.C nihh20180810Brian P. Walenz +A src/utility/files.C nihh20180810Brian P. Walenz +A src/utility/files.H nihh20180810Brian P. Walenz +A src/utility/kmers-reader.C nihh20180810Brian P. Walenz +A src/utility/kmers-writer.C nihh20180810Brian P. Walenz +A src/utility/sequence.C nihh20180810Brian P. Walenz +A src/utility/kmers-writer.C nihh20180809Brian P. Walenz +A src/pipelines/canu/OverlapMhap.pm nihh20180801Sergey Koren +A src/pipelines/trioCanu.pl nihh20180801Sergey Koren +A src/utgcns/libpbutgcns/AlnGraphBoost.C nihh20180801Sergey Koren +A src/utility/kmers-writer.C nihh20180730Brian P. Walenz +A src/utility/sequence.H nihh20180730Brian P. Walenz +A src/overlapInCore/overlapInCore-Build_Hash_Index.C nihh20180730Brian P. Walenz +A src/meryl/findSeedThreshold.C nihh20180730Brian P. Walenz +A src/meryl/meryl.C nihh20180730Brian P. Walenz +A src/meryl/merylInput.C nihh20180730Brian P. Walenz +A src/meryl/merylInput.H nihh20180730Brian P. Walenz +A src/meryl/merylOp.C nihh20180730Brian P. Walenz +A src/meryl/merylOp.H nihh20180730Brian P. Walenz +A src/meryl/meryl.C nihh20180730Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20180730Brian P. Walenz +A src/meryl/merylOp.C nihh20180730Brian P. Walenz +A src/meryl/merylOp.H nihh20180730Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180730Brian P. Walenz +A src/meryl/merylOp-countSimple.C nihh20180730Brian P. Walenz +A src/utility/kmers-exact.C nihh20180730Brian P. Walenz +A src/overlapInCore/overlapInCore.C nihh20180730Brian P. Walenz +A src/stores/sqStoreDumpFASTQ.C nihh20180730Brian P. Walenz +A src/utility/kmers-reader.C nihh20180730Brian P. Walenz +A src/utility/strings.H nihh20180727Brian P. Walenz +A src/main.mk nihh20180723Brian P. Walenz +A src/meryl/findSeedThreshold.C nihh20180723Brian P. Walenz +A src/meryl/findSeedThreshold.mk nihh20180723Brian P. Walenz +A src/meryl/lookup.C nihh20180723Brian P. Walenz +A src/utility/kmers-exact.C nihh20180723Brian P. Walenz +A src/utility/kmers.H nihh20180723Brian P. Walenz +A src/meryl/meryl.C nihh20180723Brian P. Walenz +A src/meryl/meryl.mk nihh20180723Brian P. Walenz +A src/meryl/merylInput.C nihh20180723Brian P. Walenz +A src/meryl/merylInput.H nihh20180723Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180723Brian P. Walenz +A src/meryl/merylOp-countSimple.C nihh20180723Brian P. Walenz +A src/meryl/merylOp.C nihh20180723Brian P. Walenz +A src/meryl/merylOp.H nihh20180723Brian P. Walenz +A src/bogart/AS_BAT_OverlapCache.C nihh20180723Brian P. Walenz +A src/bogart/addReadsToUnitigs.C nihh20180723Brian P. Walenz +A src/erateEstimate/erateEstimate.C nihh20180723Brian P. Walenz +A src/merTrim/merTrim.C nihh20180723Brian P. Walenz +A src/meryl-san/libkmer/existDB.C nihh20180723Brian P. Walenz +A src/meryl-san/libleaff/fastaFile.C nihh20180723Brian P. Walenz +A src/meryl-san/libleaff/fastqFile.C nihh20180723Brian P. Walenz +A src/meryl-san/libleaff/sqStoreFile.C nihh20180723Brian P. Walenz +A src/meryl-san/libmeryl-san.C nihh20180723Brian P. Walenz +A src/meryl-san/maskMers.C nihh20180723Brian P. Walenz +A src/meryl-san/meryl-build.C nihh20180723Brian P. Walenz +A src/meryl-san/meryl-san.C nihh20180723Brian P. Walenz +A src/meryl-san/positionDB.C nihh20180723Brian P. Walenz +A src/meryl-san/simple-dump.C nihh20180723Brian P. Walenz +A src/meryl-san/utility/bitPackedFile.C nihh20180723Brian P. Walenz +A src/meryl/meryl.C nihh20180723Brian P. Walenz +A src/mhap/mhapConvert.C nihh20180723Brian P. Walenz +A src/minimap/mmapConvert.C nihh20180723Brian P. Walenz +A src/overlapBasedTrimming/clearRangeFile.H nihh20180723Brian P. Walenz +A src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C nihh20180723Brian P. Walenz +A src/overlapInCore/overlapConvert.C nihh20180723Brian P. Walenz +A src/overlapInCore/overlapImport.C nihh20180723Brian P. Walenz +A src/overlapInCore/overlapPair.C nihh20180723Brian P. Walenz +A src/sequence/sequence.C nihh20180723Brian P. Walenz +A src/stores/loadCorrectedReads.C nihh20180723Brian P. Walenz +A src/stores/loadErates.C nihh20180723Brian P. Walenz +A src/stores/ovStore.C nihh20180723Brian P. Walenz +A src/stores/ovStoreBucketizer.C nihh20180723Brian P. Walenz +A src/stores/ovStoreConfig.C nihh20180723Brian P. Walenz +A src/stores/ovStoreFile.H nihh20180723Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180723Brian P. Walenz +A src/stores/ovStoreSorter.C nihh20180723Brian P. Walenz +A src/stores/ovStoreWriter.C nihh20180723Brian P. Walenz +A src/stores/sqStoreBlobWriter.H nihh20180723Brian P. Walenz +A src/stores/sqStoreConstructor.C nihh20180723Brian P. Walenz +A src/stores/sqStoreCreate.C nihh20180723Brian P. Walenz +A src/stores/sqStorePartition.C nihh20180723Brian P. Walenz +A src/stores/tgStore.C nihh20180723Brian P. Walenz +A src/stores/tgStoreLoad.C nihh20180723Brian P. Walenz +A src/utility/files-compressed.C nihh20180723Brian P. Walenz +A src/utility/files.C nihh20180723Brian P. Walenz +A src/utility/files.H nihh20180723Brian P. Walenz +A src/utility/kmers-reader.C nihh20180723Brian P. Walenz +A src/utility/objectStore.C nihh20180723Brian P. Walenz +A src/utility/sequence.C nihh20180723Brian P. Walenz +A src/wtdbg/wtdbgConvert.C nihh20180723Brian P. Walenz +A src/Makefile nihh20180723Brian P. Walenz +A src/AS_global.H nihh20180723Brian P. Walenz +A src/Makefile nihh20180723Brian P. Walenz +A src/Makefile nihh20180723Brian P. Walenz +A src/Makefile nihh20180723Brian P. Walenz +A addCopyrights.dat nihh20180721Brian P. Walenz +A src/AS_global.C nihh20180721Brian P. Walenz +A src/main.mk nihh20180721Brian P. Walenz +A src/utility/system.H nihh20180721Brian P. Walenz +A src/utility/system.H nihh20180721Brian P. Walenz +A addCopyrights.dat nihh20180721Brian P. Walenz +A src/correction/falconsense.C nihh20180721Brian P. Walenz +A src/correction/generateCorrectionLayouts.C nihh20180721Brian P. Walenz +A src/correction/readConsensus.C nihh20180721Brian P. Walenz +A src/fastq-utilities/fastqSimulate-sort.C nihh20180721Brian P. Walenz +A src/fastq-utilities/fastqSimulate.C nihh20180721Brian P. Walenz +A src/gfa/alignGFA.C nihh20180721Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20180721Brian P. Walenz +A src/main.mk nihh20180721Brian P. Walenz +A src/merTrim/merTrim.C nihh20180721Brian P. Walenz +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20180721Brian P. Walenz +A src/overlapErrorAdjustment/findErrors-Process_Olap.C nihh20180721Brian P. Walenz +A src/overlapInCore/overlapInCore-Build_Hash_Index.C nihh20180721Brian P. Walenz +A src/overlapInCore/overlapInCore-Process_Overlaps.C nihh20180721Brian P. Walenz +A src/overlapInCore/overlapPair.C nihh20180721Brian P. Walenz +A src/stores/tgTig.C nihh20180721Brian P. Walenz +A src/stores/tgTigMultiAlignDisplay.C nihh20180721Brian P. Walenz +A src/utgcns/libNDalign/NDalign.H nihh20180721Brian P. Walenz +A src/utgcns/libNNalign/NNalgorithm.C nihh20180721Brian P. Walenz +A src/utgcns/libNNalign/NNalign.C nihh20180721Brian P. Walenz +A src/utility/sequence.C nihh20180721Brian P. Walenz +A src/utility/sequence.H nihh20180721Brian P. Walenz +A src/main.mk nihh20180721Brian P. Walenz +A src/meryl/lookup.C nihh20180721Brian P. Walenz +A src/meryl/lookup.mk nihh20180721Brian P. Walenz +A src/meryl/meryl.C nihh20180721Brian P. Walenz +A src/meryl/meryl.H nihh20180721Brian P. Walenz +A src/meryl/meryl.mk nihh20180721Brian P. Walenz +A src/meryl/merylCountArray.C nihh20180721Brian P. Walenz +A src/meryl/merylCountArray.H nihh20180721Brian P. Walenz +A src/meryl/merylInput.C nihh20180721Brian P. Walenz +A src/meryl/merylInput.H nihh20180721Brian P. Walenz +A src/meryl/merylOp-count.C nihh20180721Brian P. Walenz +A src/meryl/merylOp-countSimple.C nihh20180721Brian P. Walenz +A src/meryl/merylOp-histogram.C nihh20180721Brian P. Walenz +A src/meryl/merylOp-nextMer.C nihh20180721Brian P. Walenz +A src/meryl/merylOp.C nihh20180721Brian P. Walenz +A src/meryl/merylOp.H nihh20180721Brian P. Walenz +A src/sequence/sequence.C nihh20180721Brian P. Walenz +A src/sequence/sequence.mk nihh20180721Brian P. Walenz +A src/utility/bits.C nihh20180721Brian P. Walenz +A src/utility/bits.H nihh20180721Brian P. Walenz +A src/utility/bitsTest.C nihh20180721Brian P. Walenz +A src/utility/kmers-exact.C nihh20180721Brian P. Walenz +A src/utility/kmers-reader.C nihh20180721Brian P. Walenz +A src/utility/kmers-statistics.C nihh20180721Brian P. Walenz +A src/utility/kmers-writer.C nihh20180721Brian P. Walenz +A src/utility/kmers.C nihh20180721Brian P. Walenz +A src/utility/kmers.H nihh20180721Brian P. Walenz +A src/utility/sequence.C nihh20180721Brian P. Walenz +A src/utility/sequence.H nihh20180721Brian P. Walenz +A src/main.mk nihh20180721Brian P. Walenz +A addCopyrights.dat nihh20180721Brian P. Walenz +A src/AS_global.C nihh20180721Brian P. Walenz +A src/AS_global.H nihh20180721Brian P. Walenz +A src/bogart/AS_BAT_OverlapCache.C nihh20180721Brian P. Walenz +A src/correction/readConsensus.C nihh20180721Brian P. Walenz +A src/main.mk nihh20180721Brian P. Walenz +A src/meryl-san/meryl-san.H nihh20180721Brian P. Walenz +A src/meryl-san/simple.C nihh20180721Brian P. Walenz +A src/overlapInCore/overlapPair.C nihh20180721Brian P. Walenz +D src/utility/speedCounter.H src/AS_UTL/speedCounter.H +A src/utility/speedCounter.H nihh20180721Brian P. Walenz +A src/utility/sweatShop.C nihh20180721Brian P. Walenz +A addCopyrights.dat nihh20180720Brian P. Walenz +A src/correction/errorEstimate.C nihh20180720Brian P. Walenz +A src/correction/falconsense.C nihh20180720Brian P. Walenz +A src/correction/filterCorrectionOverlaps.C nihh20180720Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20180720Brian P. Walenz +A src/main.mk nihh20180720Brian P. Walenz +A src/overlapBasedTrimming/splitReads.C nihh20180720Brian P. Walenz +A src/overlapBasedTrimming/splitReads.H nihh20180720Brian P. Walenz +A src/overlapBasedTrimming/trimReads.C nihh20180720Brian P. Walenz +A src/overlapInCore/overlapImport.C nihh20180720Brian P. Walenz +A src/overlapInCore/overlapInCore.C nihh20180720Brian P. Walenz +A src/overlapInCore/overlapInCorePartition.C nihh20180720Brian P. Walenz +A src/stores/dumpBlob.C nihh20180720Brian P. Walenz +A src/stores/loadErates.C nihh20180720Brian P. Walenz +A src/stores/ovStoreBuild.C nihh20180720Brian P. Walenz +A src/stores/ovStoreConfig.C nihh20180720Brian P. Walenz +A src/stores/ovStoreDump.C nihh20180720Brian P. Walenz +A src/stores/sqStoreCreate.C nihh20180720Brian P. Walenz +A src/stores/sqStoreDumpFASTQ.C nihh20180720Brian P. Walenz +A src/stores/tgStoreDump.C nihh20180720Brian P. Walenz +A src/utgcns/utgcns.C nihh20180720Brian P. Walenz +A src/utility/strings.H nihh20180720Brian P. Walenz +A src/bogart/AS_BAT_OverlapCache.C nihh20180720Brian P. Walenz +A src/bogart/AS_BAT_OverlapCache.H nihh20180720Brian P. Walenz +A src/erateEstimate/erateEstimate.C nihh20180720Brian P. Walenz +A src/main.mk nihh20180720Brian P. Walenz +A src/meryl-san/libkmer/positionDB-file.C nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/seqFile.H nihh20180720Brian P. Walenz +A src/stores/dumpBlob.C nihh20180720Brian P. Walenz +A src/stores/ovStore.H nihh20180720Brian P. Walenz +A src/stores/sqStore.H nihh20180720Brian P. Walenz +A src/utility/files-compressed.C nihh20180720Brian P. Walenz +A src/utility/files-compressed.H nihh20180720Brian P. Walenz +A src/utility/files.C nihh20180720Brian P. Walenz +A src/utility/files.H nihh20180720Brian P. Walenz +A src/utgcns/libNDalign/NDalign.C nihh20180720Brian P. Walenz +A addCopyrights.dat nihh20180720Brian P. Walenz +A src/main.mk nihh20180720Brian P. Walenz +A src/utility/readBuffer-implementation.H nihh20180720Brian P. Walenz +A src/utility/readBuffer.H nihh20180720Brian P. Walenz +A src/utility/writeBuffer.C nihh20180720Brian P. Walenz +A src/utility/writeBuffer.H nihh20180720Brian P. Walenz +A src/main.mk nihh20180720Brian P. Walenz +A src/meryl-san/estimate-mer-threshold.mk nihh20180720Brian P. Walenz +A src/meryl-san/existDB.mk nihh20180720Brian P. Walenz +A src/meryl-san/leaff.mk nihh20180720Brian P. Walenz +A src/meryl-san/libleaff.mk nihh20180720Brian P. Walenz +A src/meryl-san/maskMers.mk nihh20180720Brian P. Walenz +A src/meryl-san/meryl-san.mk nihh20180720Brian P. Walenz +A src/meryl-san/positionDB.mk nihh20180720Brian P. Walenz +A src/meryl-san/simple-dump.mk nihh20180720Brian P. Walenz +A src/meryl-san/simple.mk nihh20180720Brian P. Walenz +A src/utility/types.H nihh20180720Brian P. Walenz +A addCopyrights.dat nihh20180720Brian P. Walenz +A src/AS_global.C nihh20180720Brian P. Walenz +A src/AS_global.H nihh20180720Brian P. Walenz +A src/bogart/AS_BAT_Logging.H nihh20180720Brian P. Walenz +A src/bogart/addReadsToUnitigs.C nihh20180720Brian P. Walenz +A src/bogart/analyzeBest.C nihh20180720Brian P. Walenz +A src/bogus/bogusUtil.H nihh20180720Brian P. Walenz +A src/correction/errorEstimate.C nihh20180720Brian P. Walenz +A src/correction/falconsense.C nihh20180720Brian P. Walenz +A src/correction/filterCorrectionOverlaps.C nihh20180720Brian P. Walenz +A src/correction/generateCorrectionLayouts.C nihh20180720Brian P. Walenz +A src/fastq-utilities/fastqAnalyze.C nihh20180720Brian P. Walenz +A src/fastq-utilities/fastqSample.C nihh20180720Brian P. Walenz +A src/fastq-utilities/fastqSimulate-sort.C nihh20180720Brian P. Walenz +A src/fastq-utilities/fastqSimulate.C nihh20180720Brian P. Walenz +A src/gfa/alignGFA.C nihh20180720Brian P. Walenz +A src/gfa/bed.C nihh20180720Brian P. Walenz +A src/gfa/bed.H nihh20180720Brian P. Walenz +A src/gfa/gfa.C nihh20180720Brian P. Walenz +A src/gfa/gfa.H nihh20180720Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20180720Brian P. Walenz +A src/main.mk nihh20180720Brian P. Walenz +A src/merTrim/merTrimApply.C nihh20180720Brian P. Walenz +A src/meryl-san/compare-counts.C nihh20180720Brian P. Walenz +A src/meryl-san/estimate-mer-threshold.C nihh20180720Brian P. Walenz +A src/meryl-san/existDB.C nihh20180720Brian P. Walenz +A src/meryl-san/gkrpt.pl nihh20180720Brian P. Walenz +A src/meryl-san/leaff-blocks.C nihh20180720Brian P. Walenz +A src/meryl-san/leaff-duplicates.C nihh20180720Brian P. Walenz +A src/meryl-san/leaff-gc.C nihh20180720Brian P. Walenz +A src/meryl-san/leaff-partition.C nihh20180720Brian P. Walenz +A src/meryl-san/leaff-simulate.C nihh20180720Brian P. Walenz +A src/meryl-san/leaff-statistics.C nihh20180720Brian P. Walenz +A src/meryl-san/leaff.C nihh20180720Brian P. Walenz +A src/meryl-san/libkmer/existDB-create-from-fasta.C nihh20180720Brian P. Walenz +A src/meryl-san/libkmer/existDB-create-from-meryl.C nihh20180720Brian P. Walenz +A src/meryl-san/libkmer/existDB-create-from-sequence.C nihh20180720Brian P. Walenz +A src/meryl-san/libkmer/existDB-state.C nihh20180720Brian P. Walenz +A src/meryl-san/libkmer/existDB.C nihh20180720Brian P. Walenz +A src/meryl-san/libkmer/existDB.H nihh20180720Brian P. Walenz +A src/meryl-san/libkmer/percentCovered.C nihh20180720Brian P. Walenz +A src/meryl-san/libkmer/positionDB-access.C nihh20180720Brian P. Walenz +A src/meryl-san/libkmer/positionDB-dump.C nihh20180720Brian P. Walenz +A src/meryl-san/libkmer/positionDB-file.C nihh20180720Brian P. Walenz +A src/meryl-san/libkmer/positionDB-mismatch.C nihh20180720Brian P. Walenz +A src/meryl-san/libkmer/positionDB-sort.C nihh20180720Brian P. Walenz +A src/meryl-san/libkmer/positionDB.C nihh20180720Brian P. Walenz +A src/meryl-san/libkmer/positionDB.H nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/fastaFile.C nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/fastaFile.H nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/fastaStdin.C nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/fastaStdin.H nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/fastqFile.C nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/fastqFile.H nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/fastqStdin.C nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/fastqStdin.H nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/merStream.H nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/seqCache.C nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/seqCache.H nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/seqFactory.C nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/seqFactory.H nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/seqFile.H nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/seqStore.C nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/seqStore.H nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/seqStream.C nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/seqStream.H nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/sffFile.C nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/sffFile.H nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/sqStoreFile.C nihh20180720Brian P. Walenz +A src/meryl-san/libleaff/sqStoreFile.H nihh20180720Brian P. Walenz +A src/meryl-san/libmeryl-san.C nihh20180720Brian P. Walenz +A src/meryl-san/libmeryl-san.H nihh20180720Brian P. Walenz +A src/meryl-san/mapMers-depth.C nihh20180720Brian P. Walenz +A src/meryl-san/mapMers.C nihh20180720Brian P. Walenz +A src/meryl-san/maskMers.C nihh20180720Brian P. Walenz +A src/meryl-san/meryl-args.C nihh20180720Brian P. Walenz +A src/meryl-san/meryl-binaryOp.C nihh20180720Brian P. Walenz +A src/meryl-san/meryl-build.C nihh20180720Brian P. Walenz +A src/meryl-san/meryl-dump.C nihh20180720Brian P. Walenz +A src/meryl-san/meryl-estimate.C nihh20180720Brian P. Walenz +A src/meryl-san/meryl-merge-listmerge.C nihh20180720Brian P. Walenz +A src/meryl-san/meryl-merge-qsort.C nihh20180720Brian P. Walenz +A src/meryl-san/meryl-merge.C nihh20180720Brian P. Walenz +A src/meryl-san/meryl-san.C nihh20180720Brian P. Walenz +A src/meryl-san/meryl-san.H nihh20180720Brian P. Walenz +A src/meryl-san/meryl-unaryOp.C nihh20180720Brian P. Walenz +A src/meryl-san/positionDB.C nihh20180720Brian P. Walenz +A src/meryl-san/simple-dump.C nihh20180720Brian P. Walenz +A src/meryl-san/simple.C nihh20180720Brian P. Walenz +A src/mhap/mhapConvert.C nihh20180720Brian P. Walenz +A src/minimap/mmapConvert.C nihh20180720Brian P. Walenz +A src/overlapBasedTrimming/clearRangeFile.H nihh20180720Brian P. Walenz +A src/overlapErrorAdjustment/findErrors.C nihh20180720Brian P. Walenz +A src/overlapInCore/edalign.C nihh20180720Brian P. Walenz +A src/overlapInCore/overlapImport.C nihh20180720Brian P. Walenz +A src/overlapInCore/overlapInCore-Build_Hash_Index.C nihh20180720Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180720Brian P. Walenz +A src/pipelines/canu/SequenceStore.pm nihh20180720Brian P. Walenz +A src/pipelines/object-store-simulator.pl nihh20180720Brian P. Walenz +A src/stores/dumpBlob.C nihh20180720Brian P. Walenz +A src/stores/ovOverlap.H nihh20180720Brian P. Walenz +A src/stores/ovStoreConfig.C nihh20180720Brian P. Walenz +A src/stores/ovStoreDump.C nihh20180720Brian P. Walenz +A src/stores/sqStore.C nihh20180720Brian P. Walenz +A src/stores/sqStoreConstructor.C nihh20180720Brian P. Walenz +A src/stores/sqStoreCreate.C nihh20180720Brian P. Walenz +A src/stores/sqStoreCreatePartition.C nihh20180720Brian P. Walenz +A src/stores/sqStoreDumpFASTQ.C nihh20180720Brian P. Walenz +A src/stores/tgStore.C nihh20180720Brian P. Walenz +A src/stores/tgTig.C nihh20180720Brian P. Walenz +A src/utgcns/libcns/abAbacus-baseCall.C nihh20180720Brian P. Walenz +A src/utgcns/libcns/unitigConsensus.C nihh20180720Brian P. Walenz +A src/utgcns/utgcns.C nihh20180720Brian P. Walenz +A src/utility/AS_UTL_alloc.C nihh20180720Brian P. Walenz +A src/utility/AS_UTL_alloc.H nihh20180720Brian P. Walenz +A src/utility/AS_UTL_decodeRange.H nihh20180720Brian P. Walenz +A src/utility/AS_UTL_reverseComplement.C nihh20180720Brian P. Walenz +A src/utility/AS_UTL_reverseComplement.H nihh20180720Brian P. Walenz +A src/utility/AS_UTL_stackTrace.C nihh20180720Brian P. Walenz +A src/utility/AS_UTL_stackTrace.H nihh20180720Brian P. Walenz +A src/utility/AS_UTL_stackTraceTest.C nihh20180720Brian P. Walenz +A src/utility/bitEncodings.C nihh20180720Brian P. Walenz +A src/utility/bitPackedArray.C nihh20180720Brian P. Walenz +A src/utility/bitPackedArray.H nihh20180720Brian P. Walenz +A src/utility/bitPackedFile.C nihh20180720Brian P. Walenz +A src/utility/dnaAlphabets.C nihh20180720Brian P. Walenz +A src/utility/dnaAlphabets.H nihh20180720Brian P. Walenz +A src/utility/hexDump.C nihh20180720Brian P. Walenz +A src/utility/hexDump.H nihh20180720Brian P. Walenz +A src/utility/intervalList.H nihh20180720Brian P. Walenz +A src/utility/intervalListTest.C nihh20180720Brian P. Walenz +A src/utility/kMer.H nihh20180720Brian P. Walenz +A src/utility/kMerTiny.H nihh20180720Brian P. Walenz +A src/utility/memoryMappedFile.C nihh20180720Brian P. Walenz +A src/utility/memoryMappedFile.H nihh20180720Brian P. Walenz +A src/utility/memoryMappedFileTest.C nihh20180720Brian P. Walenz +A src/utility/objectStore.C nihh20180720Brian P. Walenz +A src/utility/objectStore.H nihh20180720Brian P. Walenz +A src/utility/readBuffer.H nihh20180720Brian P. Walenz +A src/utility/speedCounter.C nihh20180720Brian P. Walenz +A src/utility/stddev.H nihh20180720Brian P. Walenz +A src/utility/stddevTest.C nihh20180720Brian P. Walenz +A src/utility/sweatShop.C nihh20180720Brian P. Walenz +A src/utility/sweatShop.H nihh20180720Brian P. Walenz +A src/utility/testRand.C nihh20180720Brian P. Walenz +A src/utility/timeAndSize.C nihh20180720Brian P. Walenz +A src/utility/types.H nihh20180720Brian P. Walenz +A src/utility/writeBuffer.H nihh20180720Brian P. Walenz +A src/wtdbg/wtdbgConvert.C nihh20180720Brian P. Walenz +A src/bogart/bogart.mk nihh20180720Brian P. Walenz +A src/bogus/bogus.mk nihh20180720Brian P. Walenz +A src/bogus/bogusness.mk nihh20180720Brian P. Walenz +A src/correction/errorEstimate.mk nihh20180720Brian P. Walenz +A src/correction/falconsense.mk nihh20180720Brian P. Walenz +A src/correction/filterCorrectionLayouts.mk nihh20180720Brian P. Walenz +A src/correction/filterCorrectionOverlaps.mk nihh20180720Brian P. Walenz +A src/correction/generateCorrectionLayouts.mk nihh20180720Brian P. Walenz +A src/correction/readConsensus.mk nihh20180720Brian P. Walenz +A src/erateEstimate/erateEstimate.mk nihh20180720Brian P. Walenz +A src/fastq-utilities/fastqAnalyze.mk nihh20180720Brian P. Walenz +A src/fastq-utilities/fastqSample.mk nihh20180720Brian P. Walenz +A src/fastq-utilities/fastqSimulate-sort.mk nihh20180720Brian P. Walenz +A src/fastq-utilities/fastqSimulate.mk nihh20180720Brian P. Walenz +A src/gfa/alignGFA.mk nihh20180720Brian P. Walenz +A src/haplotyping/splitHaplotype.mk nihh20180720Brian P. Walenz +A src/main.mk nihh20180720Brian P. Walenz +A src/merTrim/merTrim.mk nihh20180720Brian P. Walenz +A src/meryl-san/estimate-mer-threshold.mk nihh20180720Brian P. Walenz +A src/meryl-san/existDB.mk nihh20180720Brian P. Walenz +A src/meryl-san/leaff.mk nihh20180720Brian P. Walenz +A src/meryl-san/libleaff.mk nihh20180720Brian P. Walenz +A src/meryl-san/maskMers.mk nihh20180720Brian P. Walenz +A src/meryl-san/meryl-san.mk nihh20180720Brian P. Walenz +A src/meryl-san/positionDB.mk nihh20180720Brian P. Walenz +A src/meryl-san/simple-dump.mk nihh20180720Brian P. Walenz +A src/meryl-san/simple.mk nihh20180720Brian P. Walenz +A src/mhap/mhapConvert.mk nihh20180720Brian P. Walenz +A src/minimap/mmapConvert.mk nihh20180720Brian P. Walenz +A src/overlapBasedTrimming/splitReads.mk nihh20180720Brian P. Walenz +A src/overlapBasedTrimming/trimReads.mk nihh20180720Brian P. Walenz +A src/overlapErrorAdjustment/correctOverlaps.mk nihh20180720Brian P. Walenz +A src/overlapErrorAdjustment/findErrors-Dump.mk nihh20180720Brian P. Walenz +A src/overlapErrorAdjustment/findErrors.mk nihh20180720Brian P. Walenz +A src/overlapInCore/edalign.mk nihh20180720Brian P. Walenz +A src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.mk nihh20180720Brian P. Walenz +A src/overlapInCore/overlapConvert.mk nihh20180720Brian P. Walenz +A src/overlapInCore/overlapImport.mk nihh20180720Brian P. Walenz +A src/overlapInCore/overlapInCore.mk nihh20180720Brian P. Walenz +A src/overlapInCore/overlapInCorePartition.mk nihh20180720Brian P. Walenz +A src/overlapInCore/overlapPair.mk nihh20180720Brian P. Walenz +A src/stores/dumpBlob.mk nihh20180720Brian P. Walenz +A src/stores/loadCorrectedReads.mk nihh20180720Brian P. Walenz +A src/stores/loadErates.mk nihh20180720Brian P. Walenz +A src/stores/loadTrimmedReads.mk nihh20180720Brian P. Walenz +A src/stores/ovStoreBucketizer.mk nihh20180720Brian P. Walenz +A src/stores/ovStoreBuild.mk nihh20180720Brian P. Walenz +A src/stores/ovStoreConfig.mk nihh20180720Brian P. Walenz +A src/stores/ovStoreDump.mk nihh20180720Brian P. Walenz +A src/stores/ovStoreIndexer.mk nihh20180720Brian P. Walenz +A src/stores/ovStoreSorter.mk nihh20180720Brian P. Walenz +A src/stores/ovStoreStats.mk nihh20180720Brian P. Walenz +A src/stores/sqStoreCreate.mk nihh20180720Brian P. Walenz +A src/stores/sqStoreCreatePartition.mk nihh20180720Brian P. Walenz +A src/stores/sqStoreDumpFASTQ.mk nihh20180720Brian P. Walenz +A src/stores/sqStoreDumpMetaData.mk nihh20180720Brian P. Walenz +A src/stores/tgStoreCompress.mk nihh20180720Brian P. Walenz +A src/stores/tgStoreCoverageStat.mk nihh20180720Brian P. Walenz +A src/stores/tgStoreDump.mk nihh20180720Brian P. Walenz +A src/stores/tgStoreFilter.mk nihh20180720Brian P. Walenz +A src/stores/tgStoreLoad.mk nihh20180720Brian P. Walenz +A src/stores/tgTigDisplay.mk nihh20180720Brian P. Walenz +A src/utgcns/utgcns.mk nihh20180720Brian P. Walenz +A src/wtdbg/wtdbgConvert.mk nihh20180720Brian P. Walenz +A src/main.mk nihh20180720Brian P. Walenz +A src/merTrim/merTrim.C nihh20180720Brian P. Walenz +A src/merTrim/merTrim.mk nihh20180720Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180720Brian P. Walenz +A src/meryl/meryl-dump.C nihh20180622Brian P. Walenz +A src/AS_UTL/dnaAlphabets.C nihh20180622Brian P. Walenz +A src/stores/ovStoreConfig.C nihh20180710Brian P. Walenz +A src/pipelines/canu/OverlapMMap.pm nihh20180710Brian P. Walenz +A src/pipelines/canu/OverlapMMap.pm nihh20180710Brian P. Walenz +A src/pipelines/canu/OverlapMhap.pm nihh20180710Brian P. Walenz +A src/pipelines/canu.pl nihh20180710Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180710Brian P. Walenz +A src/stores/ovStoreFilter.C nihh20180710Brian P. Walenz +A src/overlapInCore/overlapInCore-Build_Hash_Index.C nihh20180625Brian P. Walenz +A src/stores/ovStoreFile.H nihh20180621Brian P. Walenz +A src/stores/ovStoreConfig.C nihh20180621Brian P. Walenz +A documentation/source/faq.rst nihh20180620Sergey Koren +A documentation/source/faq.rst nihh20180620Sergey Koren +A src/pipelines/canu/Defaults.pm nihh20180619Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180619Brian P. Walenz +A src/stores/ovStoreConfig.C nihh20180619Brian P. Walenz +A src/stores/ovStore.H nihh20180619Brian P. Walenz +A src/stores/ovStoreBucketizer.C nihh20180619Brian P. Walenz +A src/stores/ovStoreBuild.C nihh20180619Brian P. Walenz +A src/stores/ovStoreFilter.C nihh20180619Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20180619Brian P. Walenz +A src/stores/ovStoreBucketizer.C nihh20180619Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180619Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180619Brian P. Walenz +A src/AS_UTL/AS_UTL_fileIO.C nihh20180614Brian P. Walenz +A src/AS_UTL/AS_UTL_fileIO.H nihh20180614Brian P. Walenz +A src/AS_UTL/AS_UTL_fileIO.C nihh20180614Brian P. Walenz +A src/AS_UTL/AS_UTL_fileIO.H nihh20180614Brian P. Walenz +A src/stores/ovStoreSorter.C nihh20180614Brian P. Walenz +A src/AS_UTL/stddev.H nihh20180614Brian P. Walenz +A src/pipelines/trioCanu.pl nihh20180613Brian P. Walenz +A src/stores/sqStoreCreate.C nihh20180611Brian P. Walenz +A src/overlapInCore/overlapImport.C nihh20180608Brian P. Walenz +A src/stores/ovStoreDump.C nihh20180608Brian P. Walenz +A src/stores/ovOverlap.C nihh20180608Brian P. Walenz +A src/stores/ovOverlap.H nihh20180608Brian P. Walenz +A src/overlapInCore/overlapImport.C nihh20180608Brian P. Walenz +A src/stores/ovOverlap.C nihh20180608Brian P. Walenz +A src/stores/ovOverlap.H nihh20180608Brian P. Walenz +A src/stores/ovStoreDump.C nihh20180608Brian P. Walenz +A src/overlapInCore/overlapInCore-Build_Hash_Index.C nihh20180608Brian P. Walenz +A src/overlapInCore/overlapInCore.C nihh20180608Brian P. Walenz +A src/overlapInCore/overlapInCore.H nihh20180608Brian P. Walenz +A src/AS_UTL/objectStore.C nihh20180607Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180608Sergey Koren +A src/AS_UTL/objectStore.C nihh20180525Sergey Koren +A src/dx-canu/src/canu.sh nihh20180525Sergey Koren +A src/pipelines/canu/Grid_DNANexus.pm nihh20180525Sergey Koren +A src/AS_UTL/readBuffer.H nihh20180523Brian P. Walenz +A documentation/source/faq.rst nihh20180522Brian P. Walenz +A documentation/source/quick-start.rst nihh20180522Brian P. Walenz +A src/AS_UTL/objectStore.C nihh20180521Sergey Koren +A src/pipelines/canu/Grid_Cloud.pm nihh20180521Sergey Koren +A src/pipelines/canu/OverlapStore.pm nihh20180521Sergey Koren +A src/dx-canu/src/canu.sh nihh20180521Sergey Koren +A src/dx-canu/dxapp.json nihh20180521Sergey Koren +A src/dx-canu/src/canu.sh nihh20180521Sergey Koren +A src/pipelines/canu/OverlapStore.pm nihh20180521Sergey Koren +A src/pipelines/canu/Defaults.pm nihh20180517Sergey Koren +A src/pipelines/canu/OverlapMhap.pm nihh20180517Sergey Koren +A src/pipelines/canu/Unitig.pm nihh20180516Brian P. Walenz +A src/overlapInCore/overlapConvert.C nihh20180516Brian P. Walenz +A src/stores/ovOverlap.C nihh20180516Brian P. Walenz +A src/stores/ovOverlap.H nihh20180516Brian P. Walenz +A src/stores/ovStoreDump.C nihh20180516Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180516Brian P. Walenz +A src/stores/ovStoreHistogram.H nihh20180516Brian P. Walenz +A src/stores/ovStore.C nihh20180516Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180516Brian P. Walenz +A src/pipelines/canu/OverlapBasedTrimming.pm nihh20180516Brian P. Walenz +A src/correction/falconsense.C nihh20180515Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180515Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20180515Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20180515Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180515Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180515Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180515Brian P. Walenz +A src/pipelines/canu/Unitig.pm nihh20180515Brian P. Walenz +A documentation/source/parameter-reference.rst nihh20180514Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20180514Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180514Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180514Brian P. Walenz +A documentation/source/parameter-reference.rst nihh20180514Brian P. Walenz +A src/pipelines/canu.pl nihh20180514Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20180514Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180514Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180514Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20180514Brian P. Walenz +A src/dx-canu/src/canu.sh nihh20180511Sergey Koren +A src/pipelines/canu/Grid_DNANexus.pm nihh20180511Sergey Koren +A src/Makefile nihh20180510Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180510Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180510Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180510Brian P. Walenz +A src/pipelines/canu/Consensus.pm nihh20180510Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180510Brian P. Walenz +A src/pipelines/canu.pl nihh20180510Brian P. Walenz +A src/pipelines/canu.pl nihh20180510Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20180510Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20180510Brian P. Walenz +A src/pipelines/canu/OverlapBasedTrimming.pm nihh20180510Brian P. Walenz +A src/pipelines/canu/SequenceStore.pm nihh20180510Brian P. Walenz +A src/pipelines/trioCanu.pl nihh20180510Brian P. Walenz +A src/pipelines/canu.pl nihh20180510Brian P. Walenz +A src/pipelines/canu.pl nihh20180510Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180510Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180510Brian P. Walenz +A src/pipelines/canu.pl nihh20180510Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180510Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180510Brian P. Walenz +A src/pipelines/object-store-simulator.pl nihh20180510Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180510Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180510Brian P. Walenz +A src/pipelines/trioCanu.pl nihh20180510Brian P. Walenz +A src/pipelines/canu/Unitig.pm nihh20180510Brian P. Walenz +A src/pipelines/canu/Unitig.pm nihh20180510Brian P. Walenz +A src/pipelines/canu/Unitig.pm nihh20180510Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20180510Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20180510Brian P. Walenz +A src/pipelines/canu/OverlapBasedTrimming.pm nihh20180510Brian P. Walenz +A src/overlapInCore/libedlib/edlib.C nihh20180508Brian P. Walenz +A src/overlapInCore/libedlib/edlib.C nihh20180508Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20180509Sergey Koren +A src/pipelines/canu/OverlapBasedTrimming.pm nihh20180509Sergey Koren +A src/pipelines/canu/Grid_Cloud.pm nihh20180509Sergey Koren +A src/dx-canu/src/canu.sh nihh20180509Sergey Koren +A src/pipelines/canu/CorrectReads.pm nihh20180509Sergey Koren +A src/pipelines/canu/OverlapBasedTrimming.pm nihh20180509Sergey Koren +A src/pipelines/canu/Grid_Cloud.pm nihh20180509Sergey Koren +A src/pipelines/canu/CorrectReads.pm nihh20180509Sergey Koren +A src/dx-canu/dxapp.json nihh20180509Sergey Koren +A src/pipelines/canu/Grid_DNANexus.pm nihh20180509Sergey Koren +A src/AS_UTL/objectStore.C nihh20180509Sergey Koren +A src/dx-canu/dxapp.json nihh20180509Sergey Koren +A src/dx-canu/src/canu.sh nihh20180509Sergey Koren +A src/pipelines/canu/Defaults.pm nihh20180509Sergey Koren +A src/pipelines/canu/Execution.pm nihh20180509Sergey Koren +A src/pipelines/canu/Grid_Cloud.pm nihh20180509Sergey Koren +A src/pipelines/canu/Grid_DNANexus.pm nihh20180509Sergey Koren +A src/pipelines/canu/OverlapStore.pm nihh20180509Sergey Koren +A src/pipelines/canu/Execution.pm nihh20180509Sergey Koren +A src/pipelines/canu/Execution.pm nihh20180509Sergey Koren +A src/stores/ovStoreConfig.C nihh20180507Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180507Brian P. Walenz +A src/stores/ovStore.C nihh20180505Brian P. Walenz +A src/stores/ovStoreFile.C nihh20180505Brian P. Walenz +A src/bogart/AS_BAT_MergeOrphans.C nihh20180504Brian P. Walenz +A buildRelease.sh nihh20180504Brian P. Walenz +A src/pipelines/object-store-simulator.pl nihh20180504Brian P. Walenz +A src/stores/sqRead.H nihh20180504Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20180504Brian P. Walenz +A src/AS_UTL/objectStore.C nihh20180504Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180504Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180504Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180504Brian P. Walenz +A src/stores/sqRead.H nihh20180504Brian P. Walenz +A src/stores/sqStore.H nihh20180504Brian P. Walenz +A src/stores/ovStoreIndexer.C nihh20180504Brian P. Walenz +A src/stores/ovStoreWriter.C nihh20180504Brian P. Walenz +A src/stores/ovStoreHistogram.H nihh20180504Brian P. Walenz +A src/stores/ovStoreFile.C nihh20180504Brian P. Walenz +A src/stores/ovStoreFile.H nihh20180504Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180504Brian P. Walenz +A src/stores/ovStoreFile.C nihh20180504Brian P. Walenz +A src/stores/ovStoreConfig.C nihh20180504Brian P. Walenz +A src/stores/ovStore.C nihh20180504Brian P. Walenz +A src/AS_UTL/objectStore.C nihh20180501Brian P. Walenz +A src/AS_UTL/objectStore.H nihh20180501Brian P. Walenz +A src/main.mk nihh20180501Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180501Brian P. Walenz +A src/stores/ovStoreFile.C nihh20180501Brian P. Walenz +A src/stores/sqStoreBlobReader.H nihh20180501Brian P. Walenz +A src/stores/ovStoreFile.C nihh20180501Brian P. Walenz +A src/stores/ovStoreFile.H nihh20180501Brian P. Walenz +A src/stores/sqStoreConstructor.C nihh20180501Brian P. Walenz +A src/stores/sqStore.H nihh20180501Brian P. Walenz +A src/stores/sqStoreBlobWriter.H nihh20180501Brian P. Walenz +A src/stores/sqStoreConstructor.C nihh20180501Brian P. Walenz +A src/stores/sqStoreInfo.C nihh20180501Brian P. Walenz +A src/pipelines/canu/OverlapErrorAdjustment.pm nihh20180501Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180501Brian P. Walenz +A src/pipelines/canu.pl nihh20180501Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180501Brian P. Walenz +A src/meryl/libleaff/sqStoreFile.C nihh20180501Brian P. Walenz +A src/AS_UTL/splitToWords.H nihh20180501Brian P. Walenz +A src/AS_UTL/splitToWordsTest.C nihh20180501Brian P. Walenz +A src/bogus/bogusUtil.C nihh20180501Brian P. Walenz +A src/correction/errorEstimate.C nihh20180501Brian P. Walenz +A src/gfa/bed.C nihh20180501Brian P. Walenz +A src/meryl/estimate-mer-threshold.C nihh20180501Brian P. Walenz +A src/mhap/mhapConvert.C nihh20180501Brian P. Walenz +A src/minimap/mmapConvert.C nihh20180501Brian P. Walenz +A src/overlapInCore/overlapImport.C nihh20180501Brian P. Walenz +A src/stores/ovStoreDump.C nihh20180501Brian P. Walenz +A src/wtdbg/wtdbgConvert.C nihh20180501Brian P. Walenz +A src/correction/falconsense.C nihh20180501Brian P. Walenz +A src/AS_UTL/AS_UTL_alloc.H nihh20180501Brian P. Walenz +A src/pipelines/canu/Consensus.pm nihh20180430Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180430Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180430Brian P. Walenz +A src/utgcns/utgcns.C nihh20180430Brian P. Walenz +A src/pipelines/canu/Consensus.pm nihh20180430Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20180430Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180430Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20180430Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180430Brian P. Walenz +A src/pipelines/canu/Output.pm nihh20180430Brian P. Walenz +A src/pipelines/canu/OverlapBasedTrimming.pm nihh20180430Brian P. Walenz +A src/pipelines/canu/OverlapErrorAdjustment.pm nihh20180430Brian P. 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Walenz +A src/utgcns/libcns/unitigConsensus.C nihh20180428Brian P. Walenz +A src/utgcns/libcns/unitigConsensus.H nihh20180428Brian P. Walenz +A src/utgcns/stashContains.C nihh20180428Brian P. Walenz +A src/utgcns/stashContains.H nihh20180428Brian P. Walenz +A src/utgcns/utgcns.C nihh20180428Brian P. Walenz +A src/stores/sqStorePartition.C nihh20180427Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20180427Brian P. Walenz +A src/pipelines/canu/Consensus.pm nihh20180425Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20180425Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20180425Brian P. Walenz +A src/pipelines/canu/Output.pm nihh20180425Brian P. Walenz +A src/pipelines/canu/Unitig.pm nihh20180425Brian P. Walenz +A src/pipelines/canu.pl nihh20180425Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20180425Brian P. Walenz +A src/correction/generateCorrectionLayouts.C nihh20180425Brian P. Walenz +A src/correction/falconsense.C nihh20180425Brian P. Walenz +A src/correction/falconsense.C nihh20180425Brian P. Walenz +A src/correction/falconConsensus-alignTag.C nihh20180425Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180425Brian P. Walenz +A src/stores/sqStoreDumpFASTQ.C nihh20180424Brian P. Walenz +A src/AS_UTL/AS_UTL_reverseComplement.C nihh20180427Sergey Koren +A src/pipelines/canu/CorrectReads.pm nihh20180423Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20180423Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180423Brian P. Walenz +A src/pipelines/canu.pl nihh20180423Brian P. Walenz +A src/pipelines/canu/Consensus.pm nihh20180423Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20180423Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180423Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180423Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20180423Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180423Brian P. 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Walenz +A src/correction/falconConsensus-alignTag.H nihh20180418Brian P. Walenz +A src/correction/falconConsensus-msa.H nihh20180418Brian P. Walenz +A src/correction/falconConsensus.C nihh20180418Brian P. Walenz +A src/correction/falconConsensus.H nihh20180418Brian P. Walenz +A src/correction/falconsense.C nihh20180418Brian P. Walenz +A src/correction/filterCorrectionLayouts.C nihh20180418Brian P. Walenz +A src/correction/filterCorrectionOverlaps.C nihh20180418Brian P. Walenz +A src/correction/generateCorrectionLayouts.C nihh20180418Brian P. Walenz +A src/correction/readConsensus.C nihh20180418Brian P. Walenz +A src/erateEstimate/erateEstimate.C nihh20180418Brian P. Walenz +A src/gfa/alignGFA.C nihh20180418Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20180418Brian P. Walenz +A src/main.mk nihh20180418Brian P. Walenz +A src/merTrim/merTrim.C nihh20180418Brian P. Walenz +A src/merTrim/merTrimApply.C nihh20180418Brian P. Walenz +A src/meryl/estimate-mer-threshold.C nihh20180418Brian P. Walenz +A src/meryl/libleaff.mk nihh20180418Brian P. Walenz +A src/meryl/libleaff/seqFactory.C nihh20180418Brian P. Walenz +A src/meryl/simple-dump.C nihh20180418Brian P. Walenz +A src/mhap/mhapConvert.C nihh20180418Brian P. Walenz +A src/minimap/mmapConvert.C nihh20180418Brian P. Walenz +A src/overlapBasedTrimming/adjustFlipped.C nihh20180418Brian P. Walenz +A src/overlapBasedTrimming/adjustOverlaps.H nihh20180418Brian P. Walenz +A src/overlapBasedTrimming/clearRangeFile.H nihh20180418Brian P. Walenz +A src/overlapBasedTrimming/splitReads-subReads.C nihh20180418Brian P. Walenz +A src/overlapBasedTrimming/splitReads-trimBad.C nihh20180418Brian P. Walenz +A src/overlapBasedTrimming/splitReads-workUnit.C nihh20180418Brian P. Walenz +A src/overlapBasedTrimming/splitReads.C nihh20180418Brian P. Walenz +A src/overlapBasedTrimming/splitReads.H nihh20180418Brian P. Walenz +A src/overlapBasedTrimming/trimReads-bestEdge.C nihh20180418Brian P. Walenz +A src/overlapBasedTrimming/trimReads-largestCovered.C nihh20180418Brian P. Walenz +A src/overlapBasedTrimming/trimReads-quality.C nihh20180418Brian P. Walenz +A src/overlapBasedTrimming/trimReads.C nihh20180418Brian P. Walenz +A src/overlapBasedTrimming/trimReads.H nihh20180418Brian P. Walenz +A src/overlapErrorAdjustment/analyzeAlignment.H nihh20180418Brian P. Walenz +A src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C nihh20180418Brian P. Walenz +A src/overlapErrorAdjustment/correctOverlaps-Read_Olaps.C nihh20180418Brian P. Walenz +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20180418Brian P. Walenz +A src/overlapErrorAdjustment/correctOverlaps.C nihh20180418Brian P. Walenz +A src/overlapErrorAdjustment/correctOverlaps.H nihh20180418Brian P. Walenz +A src/overlapErrorAdjustment/findErrors-Read_Frags.C nihh20180418Brian P. Walenz +A src/overlapErrorAdjustment/findErrors-Read_Olaps.C nihh20180418Brian P. Walenz +A src/overlapErrorAdjustment/findErrors.C nihh20180418Brian P. Walenz +A src/overlapErrorAdjustment/findErrors.H nihh20180418Brian P. Walenz +A src/overlapInCore/liboverlap/Binomial_Bound.C nihh20180418Brian P. Walenz +A src/overlapInCore/liboverlap/Display_Alignment.C nihh20180418Brian P. Walenz +A src/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C nihh20180418Brian P. Walenz +A src/overlapInCore/liboverlap/prefixEditDistance.H nihh20180418Brian P. Walenz +A src/overlapInCore/overlapConvert.C nihh20180418Brian P. Walenz +A src/overlapInCore/overlapImport.C nihh20180418Brian P. Walenz +A src/overlapInCore/overlapInCore-Build_Hash_Index.C nihh20180418Brian P. Walenz +A src/overlapInCore/overlapInCore-Process_Overlaps.C nihh20180418Brian P. Walenz +A src/overlapInCore/overlapInCore.C nihh20180418Brian P. Walenz +A src/overlapInCore/overlapInCore.H nihh20180418Brian P. Walenz +A src/overlapInCore/overlapInCorePartition.C nihh20180418Brian P. Walenz +A src/overlapInCore/overlapPair.C nihh20180418Brian P. Walenz +A src/overlapInCore/overlapReadCache.C nihh20180418Brian P. Walenz +A src/overlapInCore/overlapReadCache.H nihh20180418Brian P. Walenz +A src/pipelines/bogart-sweep.pl nihh20180418Brian P. Walenz +A src/pipelines/canu.pl nihh20180418Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/Consensus.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/ErrorEstimate.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/Grid_Cloud.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/Grid_DNANexus.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/Output.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/OverlapBasedTrimming.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/OverlapErrorAdjustment.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/OverlapInCore.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/OverlapMMap.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/OverlapMhap.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/Report.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/Unitig.pm nihh20180418Brian P. Walenz +A src/pipelines/parallel-ovl-store-test.sh nihh20180418Brian P. Walenz +A src/pipelines/trioCanu.pl nihh20180418Brian P. Walenz +A src/stores/dumpBlob.C nihh20180418Brian P. Walenz +A src/stores/loadCorrectedReads.C nihh20180418Brian P. Walenz +A src/stores/loadErates.C nihh20180418Brian P. Walenz +A src/stores/loadTrimmedReads.C nihh20180418Brian P. Walenz +A src/stores/ovOverlap.C nihh20180418Brian P. Walenz +A src/stores/ovOverlap.H nihh20180418Brian P. Walenz +A src/stores/ovStore.C nihh20180418Brian P. Walenz +A src/stores/ovStore.H nihh20180418Brian P. Walenz +A src/stores/ovStoreBucketizer.C nihh20180418Brian P. Walenz +A src/stores/ovStoreBuild.C nihh20180418Brian P. Walenz +A src/stores/ovStoreConfig.C nihh20180418Brian P. Walenz +A src/stores/ovStoreConfig.H nihh20180418Brian P. Walenz +A src/stores/ovStoreDump.C nihh20180418Brian P. Walenz +A src/stores/ovStoreFile.C nihh20180418Brian P. Walenz +A src/stores/ovStoreFile.H nihh20180418Brian P. Walenz +A src/stores/ovStoreFilter.C nihh20180418Brian P. Walenz +A src/stores/ovStoreFilter.H nihh20180418Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180418Brian P. Walenz +A src/stores/ovStoreHistogram.H nihh20180418Brian P. Walenz +A src/stores/ovStoreIndexer.C nihh20180418Brian P. Walenz +A src/stores/ovStoreSorter.C nihh20180418Brian P. Walenz +A src/stores/ovStoreStats.C nihh20180418Brian P. Walenz +A src/stores/ovStoreWriter.C nihh20180418Brian P. Walenz +A src/stores/sqLibrary.C nihh20180418Brian P. Walenz +A src/stores/tgStoreCompress.C nihh20180418Brian P. Walenz +A src/stores/tgStoreCoverageStat.C nihh20180418Brian P. Walenz +A src/stores/tgStoreDump.C nihh20180418Brian P. Walenz +A src/stores/tgStoreFilter.C nihh20180418Brian P. Walenz +A src/stores/tgStoreLoad.C nihh20180418Brian P. Walenz +A src/stores/tgTig.H nihh20180418Brian P. Walenz +A src/stores/tgTigDisplay.C nihh20180418Brian P. Walenz +A src/stores/tgTigMultiAlignDisplay.C nihh20180418Brian P. Walenz +A src/utgcns/libNDalign/Binomial_Bound.C nihh20180418Brian P. Walenz +A src/utgcns/libNDalign/NDalgorithm.H nihh20180418Brian P. Walenz +A src/utgcns/libNNalign/NNalgorithm.C nihh20180418Brian P. Walenz +A src/utgcns/libNNalign/NNalign.C nihh20180418Brian P. Walenz +A src/utgcns/libcns/abAbacus-addRead.C nihh20180418Brian P. Walenz +A src/utgcns/libcns/abAbacus.H nihh20180418Brian P. Walenz +A src/utgcns/libcns/abColumn.H nihh20180418Brian P. Walenz +A src/utgcns/libcns/abMultiAlign.C nihh20180418Brian P. Walenz +A src/utgcns/libcns/abSequence.H nihh20180418Brian P. Walenz +A src/utgcns/libcns/unitigConsensus.C nihh20180418Brian P. Walenz +A src/utgcns/libcns/unitigConsensus.H nihh20180418Brian P. Walenz +A src/utgcns/stashContains.H nihh20180418Brian P. Walenz +A src/utgcns/utgcns.C nihh20180418Brian P. Walenz +A src/wtdbg/wtdbgConvert.C nihh20180418Brian P. Walenz +A src/main.mk nihh20180418Sergey Koren +A src/pipelines/canu.pl nihh20180418Sergey Koren +A src/pipelines/canu/Configure.pm nihh20180418Sergey Koren +A src/pipelines/canu/Defaults.pm nihh20180418Sergey Koren +A src/pipelines/canu/Unitig.pm nihh20180418Sergey Koren +A src/wtdbg/wtdbgConvert.C nihh20180418Sergey Koren +A src/wtdbg/wtdbgConvert.mk nihh20180418Sergey Koren +A src/utgcns/libcns/unitigConsensus.C nihh20180418Sergey Koren +A src/overlapErrorAdjustment/findErrors-Read_Frags.C nihh20180418Brian P. Walenz +A src/overlapErrorAdjustment/findErrors-Read_Olaps.C nihh20180418Brian P. Walenz +A src/overlapErrorAdjustment/findErrors.C nihh20180418Brian P. Walenz +A src/overlapErrorAdjustment/findErrors.H nihh20180418Brian P. Walenz +A src/pipelines/canu/OverlapErrorAdjustment.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20180418Brian P. Walenz +A src/pipelines/canu/Grid_PBSTorque.pm nihh20180417Sergey Koren +A src/stores/ovStoreConfig.C nihh20180417Brian P. Walenz +A src/pipelines/canu.pl nihh20180417Brian P. Walenz +A src/minimap/mmapConvert.C nihh20180416Sergey Koren +A src/pipelines/canu/OverlapMMap.pm nihh20180416Sergey Koren +A documentation/source/faq.rst nihh20180416Brian P. Walenz +A documentation/source/parameter-reference.rst nihh20180416Brian P. Walenz +A documentation/source/parameter-reference.rst nihh20180416Brian P. Walenz +A src/bogart/bogart.C nihh20180416Brian P. Walenz +A src/AS_UTL/AS_UTL_decodeRange.H nihh20180416Brian P. Walenz +A src/bogart/AS_BAT_OptimizePositions.C nihh20180416Brian P. Walenz +A src/bogart/AS_BAT_Unitig.H nihh20180416Brian P. Walenz +A src/bogart/AS_BAT_OverlapCache.C nihh20180416Brian P. Walenz +A src/bogart/AS_BAT_OverlapCache.C nihh20180416Brian P. Walenz +A src/bogart/bogart.C nihh20180416Brian P. Walenz +A src/correction/generateCorrectionLayouts.C nihh20180416Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180416Brian P. Walenz +A src/stores/ovStoreHistogram.H nihh20180416Brian P. Walenz +A src/stores/ovStoreDump.C nihh20180416Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180416Brian P. Walenz +A src/stores/ovStoreHistogram.H nihh20180416Brian P. Walenz +A src/stores/ovStoreWriter.C nihh20180416Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180416Brian P. Walenz +A src/correction/falconsense.C nihh20180416Brian P. Walenz +A src/correction/filterCorrectionLayouts.C nihh20180416Brian P. Walenz +A src/correction/filterCorrectionOverlaps.C nihh20180416Brian P. Walenz +A src/correction/generateCorrectionLayouts.C nihh20180416Brian P. Walenz +A src/correction/readConsensus.C nihh20180416Brian P. Walenz +A src/stores/gkRead.H nihh20180416Brian P. Walenz +A src/stores/gkStore.C nihh20180416Brian P. Walenz +A src/stores/ovOverlap.H nihh20180416Brian P. Walenz +A src/stores/ovStoreDump.C nihh20180416Brian P. Walenz +A src/pipelines/canu.pl nihh20180412Sergey Koren +A src/pipelines/canu/Gatekeeper.pm nihh20180412Brian P. Walenz +A src/pipelines/canu.pl nihh20180412Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20180412Brian P. Walenz +A src/pipelines/canu/ErrorEstimate.pm nihh20180412Brian P. Walenz +A src/pipelines/canu/Gatekeeper.pm nihh20180412Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20180412Brian P. Walenz +A src/pipelines/canu/OverlapBasedTrimming.pm nihh20180412Brian P. Walenz +A src/pipelines/canu/OverlapErrorAdjustment.pm nihh20180412Brian P. Walenz +A src/pipelines/canu/OverlapMMap.pm nihh20180412Brian P. Walenz +A src/pipelines/canu/OverlapMhap.pm nihh20180412Brian P. Walenz +A src/overlapErrorAdjustment/correctOverlaps-Correct_Frags.C nihh20180412Brian P. Walenz +A src/overlapErrorAdjustment/correctOverlaps-Redo_Olaps.C nihh20180412Brian P. Walenz +A src/bogart/AS_BAT_MarkRepeatReads.C nihh20180410Brian P. Walenz +A src/pipelines/canu/Gatekeeper.pm nihh20180409Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180409Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20180409Brian P. Walenz +A src/pipelines/canu/OverlapBasedTrimming.pm nihh20180409Brian P. Walenz +A src/pipelines/canu.pl nihh20180408Brian P. Walenz +A src/pipelines/canu/Gatekeeper.pm nihh20180408Brian P. Walenz +A src/pipelines/canu/Gatekeeper.pm nihh20180408Brian P. Walenz +A src/pipelines/canu/Output.pm nihh20180408Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20180408Brian P. Walenz +A src/pipelines/canu/OverlapBasedTrimming.pm nihh20180408Brian P. Walenz +A src/pipelines/canu/Gatekeeper.pm nihh20180408Brian P. Walenz +A src/pipelines/canu/Gatekeeper.pm nihh20180408Brian P. Walenz +A documentation/source/faq.rst nihh20180406Sergey Koren +A src/AS_UTL/AS_UTL_fileIO.H nihh20180404Brian P. Walenz +A src/pipelines/canu/Configure.pm nihh20180404Brian P. Walenz +A src/stores/gkRead.H nihh20180403Brian P. Walenz +A src/stores/ovStore.C nihh20180403Brian P. Walenz +A src/stores/ovStore.H nihh20180403Brian P. Walenz +A src/stores/ovStoreBuild.C nihh20180403Brian P. Walenz +A src/stores/ovStoreConfig.C nihh20180403Brian P. Walenz +A src/bogart/AS_BAT_OverlapCache.C nihh20180403Brian P. Walenz +A src/stores/gatekeeperDumpFASTQ.C nihh20180403Brian P. Walenz +A src/pipelines/canu/OverlapErrorAdjustment.pm nihh20180403Brian P. Walenz +A src/pipelines/canu/Unitig.pm nihh20180403Brian P. Walenz +A src/AS_global.H nihh20180403Brian P. Walenz +A src/bogart/AS_BAT_Instrumentation.C nihh20180403Brian P. Walenz +A src/bogart/AS_BAT_Unitig_AddRead.C nihh20180403Brian P. Walenz +A src/bogart/bogart.C nihh20180403Brian P. Walenz +A src/fastq-utilities/fastqAnalyze.C nihh20180403Brian P. Walenz +A src/fastq-utilities/fastqSimulate.C nihh20180403Brian P. Walenz +A src/merTrim/merTrim.C nihh20180403Brian P. Walenz +A src/meryl/libleaff/seqStore.C nihh20180403Brian P. Walenz +A src/meryl/libleaff/seqStream.C nihh20180403Brian P. Walenz +A src/overlapBasedTrimming/splitReads-subReads.C nihh20180403Brian P. Walenz +A src/overlapBasedTrimming/trimReads.C nihh20180403Brian P. Walenz +A src/overlapInCore/liboverlap/Binomial_Bound.C nihh20180403Brian P. Walenz +A src/overlapInCore/liboverlap/prefixEditDistance-forward.C nihh20180403Brian P. Walenz +A src/overlapInCore/liboverlap/prefixEditDistance-reverse.C nihh20180403Brian P. Walenz +A src/overlapInCore/overlapInCore-Process_String_Overlaps.C nihh20180403Brian P. Walenz +A src/stores/tgStore.C nihh20180403Brian P. Walenz +A src/stores/tgStoreCoverageStat.C nihh20180403Brian P. Walenz +A src/stores/tgStoreFilter.C nihh20180403Brian P. Walenz +A src/utgcns/libNDalign/NDalgorithm-forward.C nihh20180403Brian P. Walenz +A src/utgcns/libNDalign/NDalgorithm-reverse.C nihh20180403Brian P. Walenz +A src/utgcns/libcns/abAbacus-applyAlignment.C nihh20180403Brian P. Walenz +A src/utgcns/libcns/abAbacus-baseCall.C nihh20180403Brian P. Walenz +A src/utgcns/libcns/unitigConsensus.C nihh20180403Brian P. Walenz +A src/utgcns/stashContains.C nihh20180403Brian P. Walenz +A src/AS_UTL/AS_UTL_fileIO.C nihh20180403Brian P. Walenz +A src/AS_global.H nihh20180403Brian P. Walenz +A src/bogart/AS_BAT_OverlapCache.C nihh20180403Brian P. Walenz +A src/erateEstimate/erateEstimate.C nihh20180403Brian P. Walenz +A src/merTrim/merTrim.C nihh20180403Brian P. Walenz +A src/merTrim/merTrimApply.C nihh20180403Brian P. Walenz +A src/overlapErrorAdjustment/findErrors.C nihh20180403Brian P. Walenz +A src/overlapErrorAdjustment/findErrors.H nihh20180403Brian P. Walenz +A src/overlapInCore/liboverlap/prefixEditDistance-forward.C nihh20180403Brian P. Walenz +A src/overlapInCore/liboverlap/prefixEditDistance-reverse.C nihh20180403Brian P. Walenz +A src/overlapInCore/overlapInCore-Build_Hash_Index.C nihh20180403Brian P. Walenz +A src/overlapInCore/overlapInCore-Find_Overlaps.C nihh20180403Brian P. Walenz +A src/overlapInCore/overlapInCore-Process_String_Overlaps.C nihh20180403Brian P. Walenz +A src/overlapInCore/overlapInCore.C nihh20180403Brian P. Walenz +A src/stores/ovStoreBucketizer.C nihh20180403Brian P. Walenz +A src/stores/ovStoreFile.C nihh20180403Brian P. Walenz +A src/stores/ovStoreSorter.C nihh20180403Brian P. Walenz +A src/stores/ovStoreWriter.C nihh20180403Brian P. Walenz +A src/stores/tgStoreLoad.C nihh20180403Brian P. Walenz +A src/utgcns/libcns/unitigConsensus.C nihh20180403Brian P. Walenz +A src/AS_UTL/AS_UTL_decodeRange.H nihh20180403Brian P. Walenz +A src/AS_global.H nihh20180403Brian P. Walenz +A src/main.mk nihh20180403Brian P. Walenz +A src/main.mk nihh20180403Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180402Brian P. Walenz +A src/pipelines/canu/Gatekeeper.pm nihh20180402Brian P. Walenz +A src/stores/gatekeeperCreate.C nihh20180402Brian P. Walenz +A src/stores/gatekeeperDumpMetaData.C nihh20180402Brian P. Walenz +A src/stores/gkRead.H nihh20180402Brian P. Walenz +A src/stores/gkStore.C nihh20180402Brian P. Walenz +A src/stores/gkStore.H nihh20180402Brian P. Walenz +A src/correction/falconsense.C nihh20180402Brian P. Walenz +A src/correction/generateCorrectionLayouts.C nihh20180402Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20180402Brian P. Walenz +A src/overlapInCore/overlapInCorePartition.C nihh20180402Brian P. Walenz +A src/stores/gatekeeperDumpFASTQ.C nihh20180402Brian P. Walenz +A src/stores/gatekeeperDumpMetaData.C nihh20180402Brian P. Walenz +A src/stores/gkRead.H nihh20180402Brian P. Walenz +A src/stores/gkStoreInfo.C nihh20180402Brian P. Walenz +A src/stores/loadCorrectedReads.C nihh20180402Brian P. Walenz +A src/correction/falconsense.C nihh20180402Brian P. Walenz +A src/correction/generateCorrectionLayouts.C nihh20180402Brian P. Walenz +A src/stores/ovStoreFile.H nihh20180402Brian P. Walenz +A src/stores/ovStoreConfig.C nihh20180402Brian P. Walenz +A src/pipelines/canu/Gatekeeper.pm nihh20180402Brian P. Walenz +A src/haplotyping/splitHaplotype.C nihh20180402Brian P. Walenz +A src/meryl/meryl-merge.C nihh20180402Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180331Sergey Koren +A src/overlapInCore/overlapInCore-Build_Hash_Index.C nihh20180330Brian P. Walenz +A src/overlapInCore/overlapInCore.C nihh20180330Brian P. Walenz +A src/overlapInCore/overlapInCore.H nihh20180330Brian P. Walenz +A src/overlapInCore/overlapInCorePartition.C nihh20180330Brian P. Walenz +A src/stores/ovStoreStats.C nihh20180330Brian P. Walenz +A src/meryl/libkmer/existDB-state.C nihh20180330Brian P. Walenz +A src/meryl/libkmer/existDB.H nihh20180330Brian P. Walenz +A documentation/source/faq.rst nihh20180329Sergey Koren +A src/pipelines/canu/Defaults.pm nihh20180329Brian P. Walenz +A src/correction/generateCorrectionLayouts.mk nihh20180329Brian P. Walenz +A src/main.mk nihh20180329Brian P. Walenz +A documentation/source/parameter-reference.rst nihh20180329Brian P. Walenz +A src/stores/ovStoreDump.C nihh20180329Brian P. Walenz +A src/stores/ovOverlap.H nihh20180329Brian P. Walenz +A src/bogart/AS_BAT_BestOverlapGraph.C nihh20180329Brian P. Walenz +A src/pipelines/canu/Defaults.pm nihh20180328Brian P. Walenz +A src/bogart/AS_BAT_OverlapCache.C nihh20180328Brian P. Walenz +A src/correction/filterCorrectionLayouts.C nihh20180328Brian P. Walenz +A src/correction/filterCorrectionOverlaps.C nihh20180328Brian P. Walenz +A src/correction/generateCorrectionLayouts.C nihh20180328Brian P. Walenz +A src/erateEstimate/erateEstimate.C nihh20180328Brian P. Walenz +A src/main.mk nihh20180328Brian P. Walenz +A src/mhap/mhapConvert.C nihh20180328Brian P. Walenz +A src/minimap/mmapConvert.C nihh20180328Brian P. Walenz +A src/overlapBasedTrimming/splitReads.C nihh20180328Brian P. Walenz +A src/overlapBasedTrimming/trimReads.C nihh20180328Brian P. Walenz +A src/overlapInCore/overlapImport.C nihh20180328Brian P. Walenz +A src/overlapInCore/overlapPair.C nihh20180328Brian P. Walenz +A src/pipelines/canu/Gatekeeper.pm nihh20180328Brian P. Walenz +A src/pipelines/canu/OverlapErrorAdjustment.pm nihh20180328Brian P. Walenz +A src/pipelines/canu/OverlapStore.pm nihh20180328Brian P. Walenz +A src/stores/loadErates.C nihh20180328Brian P. Walenz +A src/stores/loadErates.mk nihh20180328Brian P. Walenz +A src/stores/ovOverlap.C nihh20180328Brian P. Walenz +A src/stores/ovOverlap.H nihh20180328Brian P. Walenz +A src/stores/ovStore.C nihh20180328Brian P. Walenz +A src/stores/ovStore.H nihh20180328Brian P. Walenz +A src/stores/ovStoreBucketizer.C nihh20180328Brian P. Walenz +A src/stores/ovStoreBuild.C nihh20180328Brian P. Walenz +A src/stores/ovStoreConfig.C nihh20180328Brian P. Walenz +A src/stores/ovStoreConfig.H nihh20180328Brian P. Walenz +A src/stores/ovStoreDump.C nihh20180328Brian P. Walenz +A src/stores/ovStoreDumpPicture.C nihh20180328Brian P. Walenz +A src/stores/ovStoreFile.C nihh20180328Brian P. Walenz +A src/stores/ovStoreFile.H nihh20180328Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180328Brian P. Walenz +A src/stores/ovStoreHistogram.H nihh20180328Brian P. Walenz +A src/stores/ovStoreIndexer.C nihh20180328Brian P. Walenz +A src/stores/ovStoreSorter.C nihh20180328Brian P. Walenz +A src/stores/ovStoreStats.C nihh20180328Brian P. Walenz +A src/stores/ovStoreWriter.C nihh20180328Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180328Sergey Koren +A src/pipelines/canu.pl nihh20180328Sergey Koren +A src/pipelines/canu/Defaults.pm nihh20180327Sergey Koren +A src/pipelines/canu/Execution.pm nihh20180327Sergey Koren +A src/AS_UTL/AS_UTL_fileIO.C nihh20180327Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180326Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180326Brian P. Walenz +A src/overlapInCore/overlapInCorePartition.C nihh20180323Brian P. Walenz +A src/overlapInCore/overlapInCorePartition.C nihh20180323Brian P. Walenz +A src/pipelines/canu/Unitig.pm nihh20180322Brian P. Walenz +A src/pipelines/canu/Execution.pm nihh20180322Brian P. Walenz +A src/bogart/AS_BAT_DropDeadEnds.C nihh20180319Brian P. Walenz +A src/bogart/AS_BAT_MergeOrphans.C nihh20180319Brian P. Walenz +A src/bogart/AS_BAT_BestOverlapGraph.C nihh20180316Brian P. Walenz +A src/bogart/AS_BAT_BestOverlapGraph.H nihh20180316Brian P. Walenz +A src/bogart/AS_BAT_PlaceContains.C nihh20180316Brian P. Walenz +A src/bogart/AS_BAT_PopulateUnitig.C nihh20180316Brian P. Walenz +A src/bogart/AS_BAT_BestOverlapGraph.C nihh20180316Brian P. Walenz +A src/bogart/AS_BAT_OptimizePositions.C nihh20180316Brian P. Walenz +A src/pipelines/canu/Meryl.pm nihh20180316Sergey Koren +A src/main.mk nihh20180315Brian P. Walenz +A src/stores/ovStoreConfig.C nihh20180315Brian P. Walenz +A src/stores/ovStoreConfig.mk nihh20180315Brian P. Walenz +A src/stores/ovStoreHistogram.C nihh20180315Brian P. Walenz +A src/stores/ovStoreHistogram.H nihh20180315Brian P. Walenz +A src/overlapInCore/overlapImport.C nihh20180315Brian P. Walenz +A src/stores/loadCorrectedReads.C nihh20180315Brian P. Walenz +A src/AS_UTL/writeBuffer.H nihh20180315Brian P. Walenz +A src/stores/gkRead.H nihh20180314Brian P. Walenz +A src/stores/gkStore.C nihh20180314Brian P. Walenz +A src/stores/gkStoreEncode.C nihh20180314Brian P. Walenz +A addCopyrights.dat nihh20180313Brian P. Walenz +A src/main.mk nihh20180313Brian P. Walenz +A src/stores/gkStore.C nihh20180313Brian P. Walenz +A src/stores/gkStore.H nihh20180313Brian P. Walenz +A src/stores/gkStoreConstructor.C nihh20180313Brian P. Walenz +A src/stores/gkStoreInfo.C nihh20180313Brian P. Walenz +A src/meryl/libleaff/gkStoreFile.C nihh20180313Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20180313Brian P. Walenz +A src/pipelines/canu/Gatekeeper.pm nihh20180313Brian P. Walenz +A src/pipelines/canu/HaplotypeReads.pm nihh20180313Brian P. Walenz +A src/stores/gatekeeperDumpMetaData.C nihh20180313Brian P. Walenz +A src/stores/gatekeeperPartition.C nihh20180313Brian P. Walenz +A src/stores/gkRead.H nihh20180313Brian P. Walenz +A src/stores/gkStore.C nihh20180313Brian P. Walenz +A src/stores/gkStore.H nihh20180313Brian P. Walenz +A src/stores/gkStoreBlobReader.H nihh20180313Brian P. Walenz +A src/stores/gkStoreBlobWriter.H nihh20180313Brian P. Walenz +A src/stores/gkStoreConstructor.C nihh20180313Brian P. Walenz +A src/stores/gkStorePartition.C nihh20180313Brian P. Walenz +A src/AS_UTL/AS_UTL_fileIO.C nihh20180313Brian P. Walenz +A src/AS_UTL/AS_UTL_fileIO.H nihh20180313Brian P. Walenz +A src/pipelines/canu/CorrectReads.pm nihh20180313Brian P. Walenz +A src/stores/loadCorrectedReads.C nihh20180313Brian P. Walenz +A documentation/source/quick-start.rst nihh20180312Sergey Koren +A src/stores/ovStore.H nihh20180308Brian P. Walenz +A src/stores/ovStoreBuild.C nihh20180308Brian P. Walenz +A src/stores/ovStoreFilter.C nihh20180308Brian P. Walenz +A src/utgcns/libcns/unitigConsensus.C nihh20180308Brian P. Walenz +A documentation/source/history.rst nihh20180308Brian P. Walenz +A documentation/source/canu-pipeline-17.svg nihh20180308Brian P. Walenz +A documentation/source/canu-pipeline-20.svg nihh20180308Brian P. Walenz +A src/AS_UTL/readBuffer.C nihh20180308Brian P. Walenz +A src/AS_UTL/readBuffer.H nihh20180308Brian P. Walenz +A src/AS_UTL/AS_UTL_alloc.H nihh20180308Brian P. Walenz +A src/stores/gkStore.C nihh20180308Brian P. Walenz +A src/stores/gkStoreConstructor.C nihh20180308Brian P. Walenz +A documentation/source/conf.py nihh20180227Brian P. Walenz +A src/canu_version_update.pl nihh20180227Brian P. Walenz +A addCopyrights-BuildData.pl nihh20180227Brian P. Walenz +A addCopyrights.dat nihh20180227Brian P. Walenz