[med-svn] [canu] branch upstream updated (bce57ac -> 71abef9)
Afif Elghraoui
afif at moszumanska.debian.org
Tue Mar 21 02:53:22 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch upstream
in repository canu.
from bce57ac Imported Upstream version 1.3+dfsg
new 71abef9 Imported Upstream version 1.4+dfsg
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
README.citation | 3 +-
README.md | 21 +-
addCopyrights-BuildData.pl | 1 +
addCopyrights.dat | 868 +++++
addCopyrights.pl | 36 +-
documentation/source/canu-overlaps.svg | 2836 ++++++++++++++++
documentation/source/canu-pipeline.svg | 3528 ++++++++++++++++++++
documentation/source/faq.rst | 249 +-
documentation/source/index.rst | 21 +-
documentation/source/overlap_transformations.svg | 500 +++
documentation/source/overlaps.svg | 384 +++
documentation/source/parameter-reference.rst | 17 +
documentation/source/pipeline.rst | 30 +-
documentation/source/quick-start.rst | 2 +-
documentation/source/repeat-spanned.svg | 214 ++
documentation/source/repeat-unspanned.svg | 232 ++
documentation/source/tutorial.rst | 46 +-
src/AS_RUN/fragmentDepth.C | 466 ---
src/AS_RUN/replaceIIDwithName-overlapDump.pl | 70 -
src/AS_RUN/replaceUIDwithName-fastq.pl | 153 -
src/AS_RUN/replaceUIDwithName-posmap.pl | 98 -
src/AS_UTL/AS_UTL_alloc.C | 48 +-
src/AS_UTL/AS_UTL_alloc.H | 34 +-
src/AS_UTL/AS_UTL_fileIO.C | 224 +-
src/AS_UTL/AS_UTL_fileIO.H | 22 +
src/AS_UTL/AS_UTL_stackTrace.C | 2 +-
src/AS_UTL/bitPackedArray.C | 8 +-
src/AS_UTL/bitPackedArray.H | 24 +-
src/AS_UTL/bitPackedFile.C | 21 +-
src/AS_UTL/bitPackedFile.H | 6 +-
src/AS_UTL/hexDump.C | 85 +
.../SimpleAligner.H => AS_UTL/hexDump.H} | 18 +-
src/AS_UTL/intervalList.H | 8 +-
src/AS_UTL/intervalListTest.C | 42 +-
src/AS_UTL/kMer.C | 4 +-
src/AS_UTL/kMerHuge.H | 14 +-
src/AS_UTL/memoryMappedFile.H | 4 +-
src/AS_UTL/mt19937ar.C | 8 +
src/AS_UTL/mt19937ar.H | 1 +
src/AS_UTL/mt19937arTest.C | 19 +
src/AS_UTL/readBuffer.C | 6 +-
src/AS_UTL/stddev.H | 16 +-
src/AS_UTL/sweatShop.C | 18 +-
src/AS_UTL/writeBuffer.H | 93 +
src/AS_global.C | 40 +-
src/AS_global.H | 56 +-
src/Makefile | 8 +-
src/bogart/AS_BAT_AssemblyGraph.C | 971 ++++++
src/bogart/AS_BAT_AssemblyGraph.H | 133 +
src/bogart/AS_BAT_BestOverlapGraph.C | 592 ++--
src/bogart/AS_BAT_BestOverlapGraph.H | 122 +-
src/bogart/AS_BAT_ChunkGraph.C | 144 +-
src/bogart/AS_BAT_ChunkGraph.H | 24 +-
src/bogart/AS_BAT_CreateUnitigs.C | 514 +++
...{AS_BAT_PopBubbles.H => AS_BAT_CreateUnitigs.H} | 41 +-
src/bogart/AS_BAT_FragmentInfo.C | 179 -
src/bogart/AS_BAT_Instrumentation.C | 441 +--
src/bogart/AS_BAT_Instrumentation.H | 16 +-
src/bogart/AS_BAT_Logging.C | 91 +-
src/bogart/AS_BAT_Logging.H | 15 +-
src/bogart/AS_BAT_MarkRepeatReads.C | 1276 ++++---
src/bogart/AS_BAT_MarkRepeatReads.H | 10 +-
.../{AS_BAT_PopBubbles.C => AS_BAT_MergeOrphans.C} | 517 ++-
.../{AS_BAT_PopBubbles.H => AS_BAT_MergeOrphans.H} | 10 +-
src/bogart/AS_BAT_MergeUnitigs.C | 246 --
src/bogart/AS_BAT_Outputs.C | 464 +--
src/bogart/AS_BAT_Outputs.H | 15 +-
src/bogart/AS_BAT_OverlapCache.C | 1104 +++---
src/bogart/AS_BAT_OverlapCache.H | 124 +-
src/bogart/AS_BAT_PlaceContains.C | 105 +-
src/bogart/AS_BAT_PlaceContains.H | 8 +-
src/bogart/AS_BAT_PlaceFragUsingOverlaps.C | 600 ----
src/bogart/AS_BAT_PlaceReadUsingOverlaps.C | 688 ++++
...gOverlaps.H => AS_BAT_PlaceReadUsingOverlaps.H} | 102 +-
src/bogart/AS_BAT_PopBubbles.txt | 2 +-
src/bogart/AS_BAT_PopulateUnitig.C | 117 +-
src/bogart/AS_BAT_PopulateUnitig.H | 4 +-
src/bogart/AS_BAT_PromoteToSingleton.C | 46 +-
src/bogart/AS_BAT_PromoteToSingleton.H | 2 +-
src/bogart/AS_BAT_ReadInfo.C | 83 +
.../{AS_BAT_FragmentInfo.H => AS_BAT_ReadInfo.H} | 73 +-
src/bogart/AS_BAT_ReconstructRepeats.C | 94 -
src/bogart/AS_BAT_SetParentAndHang.C | 28 +-
src/bogart/AS_BAT_SetParentAndHang.H | 4 +-
src/bogart/AS_BAT_SplitDiscontinuous.C | 219 +-
src/bogart/AS_BAT_SplitDiscontinuous.H | 5 +-
src/bogart/AS_BAT_TigGraph.C | 463 +++
.../{AS_BAT_PopBubbles.H => AS_BAT_TigGraph.H} | 19 +-
.../{AS_BAT_UnitigVector.C => AS_BAT_TigVector.C} | 73 +-
.../{AS_BAT_UnitigVector.H => AS_BAT_TigVector.H} | 43 +-
src/bogart/AS_BAT_Unitig.C | 243 +-
src/bogart/AS_BAT_Unitig.H | 111 +-
...AT_Unitig_AddFrag.C => AS_BAT_Unitig_AddRead.C} | 35 +-
src/bogart/AS_BAT_Unitig_PlaceFragUsingEdges.C | 275 --
src/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C | 270 ++
src/bogart/addReadsToUnitigs.C | 31 +-
src/bogart/analyzeBest.C | 14 +-
src/bogart/bogart.C | 360 +-
src/bogart/bogart.mk | 17 +-
src/bogart/buildGraph.C | 403 ---
src/bogart/buildGraph.mk | 19 -
src/bogart/findOverlappingReads.pl | 120 +
.../plotErrorProfile.pl} | 52 +-
src/bogus/bogus.C | 16 +-
src/bogus/bogusness.C | 4 +-
src/correction/filterCorrectionOverlaps.C | 34 +-
src/correction/generateCorrectionLayouts.C | 20 +-
src/erateEstimate/erateEstimate.C | 54 +-
src/falcon_sense/createFalconSenseInputs.C | 4 +-
src/falcon_sense/falcon_sense.C | 9 +-
src/falcon_sense/outputFalcon.C | 4 +-
src/fastq-utilities/fastqAnalyze.C | 18 +-
src/fastq-utilities/fastqSample.C | 41 +-
src/fastq-utilities/fastqSimulate-sort.C | 4 +-
src/fastq-utilities/fastqSimulate.C | 31 +-
src/main.mk | 23 +-
src/merTrim/merTrim.C | 30 +-
src/merTrim/merTrimResult.H | 4 +-
src/mercy/mercy-regions.C | 30 +-
src/mercy/mercy.C | 44 +-
src/meryl/compare-counts.C | 6 +-
src/meryl/estimate-mer-threshold.C | 26 +-
src/meryl/leaff-blocks.C | 10 +-
src/meryl/leaff-duplicates.C | 14 +-
src/meryl/leaff-gc.C | 6 +-
src/meryl/leaff-partition.C | 22 +-
src/meryl/leaff-statistics.C | 24 +-
src/meryl/leaff.C | 22 +-
src/meryl/libleaff/fastaFile.C | 19 +-
src/meryl/libleaff/fastaStdin.C | 6 +-
src/meryl/libleaff/fastqFile.C | 21 +-
src/meryl/libleaff/fastqStdin.C | 9 +-
src/meryl/libleaff/gkStoreFile.C | 2 +
src/meryl/libleaff/seqCache.C | 8 +-
src/meryl/libleaff/seqFactory.C | 8 +-
src/meryl/libleaff/seqStore.C | 20 +-
src/meryl/libleaff/seqStream.C | 24 +-
src/meryl/libleaff/sffFile.C | 5 +
src/meryl/libmeryl.C | 70 +-
src/meryl/libmeryl.H | 4 +
src/meryl/maskMers.C | 33 +-
src/meryl/{simple.mk => maskMers.mk} | 4 +-
src/meryl/meryl-args.C | 24 +-
src/meryl/meryl-binaryOp.C | 8 +-
src/meryl/meryl-build-threads.C | 123 -
src/meryl/meryl-build.C | 166 +-
src/meryl/meryl-dump.C | 26 +-
src/meryl/meryl-estimate.C | 6 +-
src/meryl/meryl-merge.C | 6 +-
src/meryl/meryl.H | 2 -
src/meryl/meryl.mk | 1 -
src/meryl/simple.C | 12 +-
src/mhap/mhap.mk | 4 +-
src/mhap/mhapConvert.C | 16 +-
src/minimap/mmapConvert.C | 6 +-
src/overlapBasedTrimming/splitReads-subReads.C | 2 +-
src/overlapBasedTrimming/splitReads.C | 62 +-
src/overlapBasedTrimming/trimReads-bestEdge.C | 6 +-
.../trimReads-largestCovered.C | 8 +-
src/overlapBasedTrimming/trimReads-quality.C | 4 +-
src/overlapBasedTrimming/trimReads.C | 32 +-
src/overlapBasedTrimming/trimStat.H | 6 +-
src/overlapErrorAdjustment/analyzeAlignment.C | 28 +-
.../correctOverlaps-Correct_Frags.C | 12 +-
.../correctOverlaps-Prefix_Edit_Distance.C | 2 +-
.../correctOverlaps-Read_Olaps.C | 6 +-
.../correctOverlaps-Redo_Olaps.C | 20 +-
src/overlapErrorAdjustment/correctOverlaps.C | 7 +-
src/overlapErrorAdjustment/correctOverlaps.H | 13 +-
.../findErrors-Process_Olap.C | 11 +-
src/overlapErrorAdjustment/findErrors-Read_Frags.C | 10 +-
src/overlapErrorAdjustment/findErrors-Read_Olaps.C | 6 +-
src/overlapErrorAdjustment/findErrors.C | 84 +-
src/overlapErrorAdjustment/findErrors.H | 20 +-
src/overlapInCore/libedlib/edlib.C | 1394 ++++++++
src/overlapInCore/libedlib/edlib.H | 270 ++
src/overlapInCore/overlapConvert.C | 13 +-
src/overlapInCore/overlapImport.C | 95 +-
src/overlapInCore/overlapInCore-Build_Hash_Index.C | 36 +-
src/overlapInCore/overlapInCore-Find_Overlaps.C | 16 +-
src/overlapInCore/overlapInCore-Output.C | 28 +-
src/overlapInCore/overlapInCore-Process_Overlaps.C | 52 +-
.../overlapInCore-Process_String_Overlaps.C | 18 +
src/overlapInCore/overlapInCore.C | 129 +-
src/overlapInCore/overlapInCore.H | 18 +-
src/overlapInCore/overlapInCorePartition.C | 92 +-
src/overlapInCore/overlapPair.C | 377 +--
src/overlapInCore/overlapPair.mk | 2 +-
src/overlapInCore/overlapReadCache.C | 6 +-
src/pipelines/canu.pl | 81 +-
src/pipelines/canu/Configure.pm | 14 +-
src/pipelines/canu/Consensus.pm | 354 +-
src/pipelines/canu/CorrectReads.pm | 94 +-
src/pipelines/canu/Defaults.pm | 495 ++-
src/pipelines/canu/ErrorEstimate.pm | 6 +-
src/pipelines/canu/Execution.pm | 534 ++-
src/pipelines/canu/Gatekeeper.pm | 60 +-
src/pipelines/canu/Grid.pm | 11 +-
src/pipelines/canu/Grid_PBSTorque.pm | 141 +-
src/pipelines/canu/Grid_Slurm.pm | 10 +-
src/pipelines/canu/HTML.pm | 255 +-
src/pipelines/canu/Meryl.pm | 15 +-
src/pipelines/canu/Output.pm | 178 +-
src/pipelines/canu/OverlapErrorAdjustment.pm | 82 +-
src/pipelines/canu/OverlapInCore.pm | 35 +-
src/pipelines/canu/OverlapMMap.pm | 41 +-
src/pipelines/canu/OverlapMhap.pm | 63 +-
src/pipelines/canu/OverlapStore.pm | 88 +-
src/pipelines/canu/Unitig.pm | 66 +-
src/pipelines/install-perl-libraries.sh | 110 -
src/pipelines/sanity/build-all-wgs-revisions.pl | 173 -
src/pipelines/sanity/compile-all-wgs-revisions.pl | 201 --
src/pipelines/sanity/sanity-asm-done.pl | 132 -
src/pipelines/sanity/sanity-get-next-date.pl | 66 -
src/pipelines/sanity/sanity-purge-old.pl | 210 --
src/pipelines/sanity/sanity-update-reference.pl | 93 -
src/pipelines/sanity/sanity.pl | 500 ++-
src/pipelines/sanity/sanity.sh | 77 +-
src/stores/gatekeeperCreate.C | 155 +-
src/stores/gatekeeperDumpFASTQ.C | 56 +-
src/stores/gatekeeperDumpMetaData.C | 10 +-
src/stores/gatekeeperPartition.C | 173 +-
src/stores/gkStore.C | 485 +--
src/stores/gkStore.H | 149 +-
src/stores/libsnappy/snappy-internal.h | 237 ++
src/stores/libsnappy/snappy-sinksource.cc | 104 +
src/stores/libsnappy/snappy-sinksource.h | 207 ++
src/stores/libsnappy/snappy-stubs-internal.cc | 42 +
src/stores/libsnappy/snappy-stubs-internal.h | 553 +++
src/stores/libsnappy/snappy-stubs-public.h | 125 +
src/stores/libsnappy/snappy.cc | 1400 ++++++++
src/stores/libsnappy/snappy.h | 228 ++
src/stores/ovOverlap.C | 16 +-
src/stores/{ovStore.H => ovOverlap.H} | 408 +--
src/stores/ovStore.C | 1150 +------
src/stores/ovStore.H | 650 ++--
src/stores/ovStoreBucketizer.C | 109 +-
src/stores/ovStoreBuild.C | 373 ++-
src/stores/ovStoreDump.C | 143 +-
src/stores/ovStoreFile.C | 416 ++-
src/stores/ovStoreFile.H | 120 +
src/stores/ovStoreFilter.C | 293 ++
.../ovStoreFilter.H} | 16 +-
src/stores/ovStoreHistogram.C | 447 +++
src/stores/ovStoreHistogram.H | 115 +
src/stores/ovStoreIndexer.C | 97 +-
src/stores/ovStoreSorter.C | 209 +-
src/stores/ovStoreStats.C | 38 +-
src/stores/ovStoreWriter.C | 757 +++++
src/stores/tgStore.C | 25 +-
src/stores/tgStore.H | 4 +-
src/stores/tgStoreCompress.C | 8 +-
src/stores/tgStoreCoverageStat.C | 8 +-
src/stores/tgStoreDump.C | 59 +-
src/stores/tgStoreFilter.C | 20 +-
src/stores/tgTig.C | 55 +-
src/stores/tgTig.H | 2 +
src/stores/tgTigMultiAlignDisplay.C | 10 +-
src/stores/tgTigSizeAnalysis.C | 9 +-
src/utgcns/libNDFalcon/dw.C | 6 +
src/utgcns/libNDFalcon/dw.H | 2 -
src/utgcns/libNDalign/NDalign.C | 2 +-
src/utgcns/libcns/abAbacus-refine.C | 17 +-
src/utgcns/libcns/unitigConsensus.C | 290 +-
src/utgcns/libpbutgcns/SimpleAligner.C | 59 -
src/utgcns/stashContains.C | 15 +-
src/utgcns/stashContains.H | 4 +-
src/utgcns/utgcns.C | 19 +-
268 files changed, 27362 insertions(+), 13117 deletions(-)
create mode 100644 documentation/source/canu-overlaps.svg
create mode 100644 documentation/source/canu-pipeline.svg
create mode 100644 documentation/source/overlap_transformations.svg
create mode 100644 documentation/source/overlaps.svg
create mode 100644 documentation/source/repeat-spanned.svg
create mode 100644 documentation/source/repeat-unspanned.svg
delete mode 100644 src/AS_RUN/fragmentDepth.C
delete mode 100644 src/AS_RUN/replaceIIDwithName-overlapDump.pl
delete mode 100644 src/AS_RUN/replaceUIDwithName-fastq.pl
delete mode 100644 src/AS_RUN/replaceUIDwithName-posmap.pl
create mode 100644 src/AS_UTL/hexDump.C
rename src/{utgcns/libpbutgcns/SimpleAligner.H => AS_UTL/hexDump.H} (75%)
create mode 100644 src/AS_UTL/mt19937arTest.C
create mode 100644 src/AS_UTL/writeBuffer.H
create mode 100644 src/bogart/AS_BAT_AssemblyGraph.C
create mode 100644 src/bogart/AS_BAT_AssemblyGraph.H
create mode 100644 src/bogart/AS_BAT_CreateUnitigs.C
copy src/bogart/{AS_BAT_PopBubbles.H => AS_BAT_CreateUnitigs.H} (57%)
delete mode 100644 src/bogart/AS_BAT_FragmentInfo.C
rename src/bogart/{AS_BAT_PopBubbles.C => AS_BAT_MergeOrphans.C} (53%)
copy src/bogart/{AS_BAT_PopBubbles.H => AS_BAT_MergeOrphans.H} (84%)
delete mode 100644 src/bogart/AS_BAT_MergeUnitigs.C
delete mode 100644 src/bogart/AS_BAT_PlaceFragUsingOverlaps.C
create mode 100644 src/bogart/AS_BAT_PlaceReadUsingOverlaps.C
rename src/bogart/{AS_BAT_PlaceFragUsingOverlaps.H => AS_BAT_PlaceReadUsingOverlaps.H} (53%)
create mode 100644 src/bogart/AS_BAT_ReadInfo.C
rename src/bogart/{AS_BAT_FragmentInfo.H => AS_BAT_ReadInfo.H} (53%)
delete mode 100644 src/bogart/AS_BAT_ReconstructRepeats.C
create mode 100644 src/bogart/AS_BAT_TigGraph.C
rename src/bogart/{AS_BAT_PopBubbles.H => AS_BAT_TigGraph.H} (70%)
rename src/bogart/{AS_BAT_UnitigVector.C => AS_BAT_TigVector.C} (68%)
rename src/bogart/{AS_BAT_UnitigVector.H => AS_BAT_TigVector.H} (57%)
rename src/bogart/{AS_BAT_Unitig_AddFrag.C => AS_BAT_Unitig_AddRead.C} (70%)
delete mode 100644 src/bogart/AS_BAT_Unitig_PlaceFragUsingEdges.C
create mode 100644 src/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C
delete mode 100644 src/bogart/buildGraph.C
delete mode 100644 src/bogart/buildGraph.mk
create mode 100644 src/bogart/findOverlappingReads.pl
rename src/{pipelines/sanity/build-all-kmer-revisions.pl => bogart/plotErrorProfile.pl} (51%)
copy src/meryl/{simple.mk => maskMers.mk} (91%)
delete mode 100644 src/meryl/meryl-build-threads.C
create mode 100644 src/overlapInCore/libedlib/edlib.C
create mode 100644 src/overlapInCore/libedlib/edlib.H
delete mode 100755 src/pipelines/install-perl-libraries.sh
delete mode 100644 src/pipelines/sanity/build-all-wgs-revisions.pl
delete mode 100644 src/pipelines/sanity/compile-all-wgs-revisions.pl
delete mode 100755 src/pipelines/sanity/sanity-asm-done.pl
delete mode 100644 src/pipelines/sanity/sanity-get-next-date.pl
delete mode 100644 src/pipelines/sanity/sanity-purge-old.pl
delete mode 100644 src/pipelines/sanity/sanity-update-reference.pl
create mode 100644 src/stores/libsnappy/snappy-internal.h
create mode 100644 src/stores/libsnappy/snappy-sinksource.cc
create mode 100644 src/stores/libsnappy/snappy-sinksource.h
create mode 100644 src/stores/libsnappy/snappy-stubs-internal.cc
create mode 100644 src/stores/libsnappy/snappy-stubs-internal.h
create mode 100644 src/stores/libsnappy/snappy-stubs-public.h
create mode 100644 src/stores/libsnappy/snappy.cc
create mode 100644 src/stores/libsnappy/snappy.h
copy src/stores/{ovStore.H => ovOverlap.H} (51%)
create mode 100644 src/stores/ovStoreFile.H
create mode 100644 src/stores/ovStoreFilter.C
rename src/{bogart/AS_BAT_MergeUnitigs.H => stores/ovStoreFilter.H} (74%)
create mode 100644 src/stores/ovStoreHistogram.C
create mode 100644 src/stores/ovStoreHistogram.H
create mode 100644 src/stores/ovStoreWriter.C
delete mode 100644 src/utgcns/libpbutgcns/SimpleAligner.C
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