[med-svn] [canu] branch master updated (c6b3703 -> f6f924b)
Afif Elghraoui
afif at moszumanska.debian.org
Tue Mar 21 02:57:58 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch master
in repository canu.
from c6b3703 Add missing copyright info
new a8dd664 Imported Upstream version 1.4+dfsg
new 757ffd0 d/copyright: Drop Files-Excluded entries for files removed upstream
new e9a8c24 Refresh patches
new f6f924b Prepare new revision
The 4 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 +-
debian/changelog | 8 +
debian/copyright | 3 -
debian/patches/external-deps.patch | 2 +-
debian/patches/use-debian-mhap-at-runtime.patch | 12 +-
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 +-
272 files changed, 27377 insertions(+), 13127 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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