[med-svn] [canu] 03/06: Merge tag 'upstream/1.3+dfsg'
Afif Elghraoui
afif at moszumanska.debian.org
Wed Jul 13 15:49:18 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository canu.
commit 5661d4f844a1624655646b4ecc1afddd42dab381
Merge: 7ec4c5f bce57ac
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Wed Jul 13 07:30:13 2016 -0700
Merge tag 'upstream/1.3+dfsg'
Upstream version 1.3+dfsg
README.md | 32 +-
addCopyrights-BuildData.pl | 10 +-
addCopyrights.dat | 3119 +++-----------------
addCopyrights.pl | 2 +-
documentation/source/commands/bogart.rst | 34 +-
.../source/commands/gatekeeperDumpFASTQ.rst | 1 +
documentation/source/commands/ovStoreDump.rst | 10 +-
documentation/source/conf.py | 4 +-
documentation/source/faq.rst | 124 +
documentation/source/index.rst | 2 +
documentation/source/parameter-reference.rst | 124 +-
documentation/source/quick-start.rst | 140 +-
documentation/source/tutorial.rst | 27 +-
src/AS_UTL/AS_UTL_stackTrace.C | 14 +-
src/AS_UTL/intervalList.H | 6 +-
.../intervalListTest.C} | 56 +-
src/AS_UTL/memoryMappedFile.H | 8 +-
src/AS_UTL/stddev.H | 92 +-
src/AS_UTL/stddevTest.C | 116 +
src/AS_global.H | 6 +
src/Makefile | 39 +-
src/bogart/AS_BAT_BestOverlapGraph.C | 1015 +++----
src/bogart/AS_BAT_BestOverlapGraph.H | 192 +-
src/bogart/AS_BAT_Breaking.C | 332 ---
src/bogart/AS_BAT_Breaking.H | 112 -
src/bogart/AS_BAT_ChunkGraph.C | 28 +-
src/bogart/AS_BAT_ChunkGraph.H | 14 +-
src/bogart/AS_BAT_Datatypes.H | 339 ---
src/bogart/AS_BAT_FragmentInfo.C | 18 +-
src/bogart/AS_BAT_FragmentInfo.H | 123 +
src/bogart/AS_BAT_Instrumentation.C | 494 +++-
src/bogart/AS_BAT_Instrumentation.H | 3 +-
src/bogart/AS_BAT_IntersectBubble.C | 660 -----
src/bogart/AS_BAT_IntersectSplit.C | 334 ---
src/bogart/AS_BAT_IntersectSplit.H | 151 -
src/bogart/AS_BAT_Joining.C | 405 ---
src/bogart/AS_BAT_Logging.C | 76 +-
src/bogart/AS_BAT_Logging.H | 17 +-
src/bogart/AS_BAT_MarkRepeatReads.C | 1133 +++++++
...BAT_PlaceZombies.H => AS_BAT_MarkRepeatReads.H} | 27 +-
src/bogart/AS_BAT_MergeSplitJoin.C | 1763 -----------
src/bogart/AS_BAT_MergeSplitJoin.H | 57 -
src/bogart/AS_BAT_MergeUnitigs.C | 246 ++
.../stddev.C => bogart/AS_BAT_MergeUnitigs.H} | 24 +-
src/bogart/AS_BAT_Outputs.C | 490 +--
src/bogart/AS_BAT_Outputs.H | 17 +-
src/bogart/AS_BAT_OverlapCache.C | 67 +-
src/bogart/AS_BAT_OverlapCache.H | 70 +-
src/bogart/AS_BAT_PlaceContains.C | 279 +-
src/bogart/AS_BAT_PlaceContains.H | 11 +-
src/bogart/AS_BAT_PlaceFragUsingOverlaps.C | 501 +---
src/bogart/AS_BAT_PlaceFragUsingOverlaps.H | 13 +-
src/bogart/AS_BAT_PlaceZombies.C | 110 -
src/bogart/AS_BAT_PopBubbles.C | 679 +++++
.../{AS_BAT_Joining.H => AS_BAT_PopBubbles.H} | 27 +-
src/bogart/AS_BAT_PopBubbles.txt | 87 +
src/bogart/AS_BAT_PopulateUnitig.C | 54 +-
src/bogart/AS_BAT_PromoteToSingleton.C | 4 +-
.../AS_BAT_PromoteToSingleton.H} | 18 +-
src/bogart/AS_BAT_ReconstructRepeats.C | 15 +-
src/bogart/AS_BAT_RepeatJunctionEvidence.H | 232 --
src/bogart/AS_BAT_SetParentAndHang.C | 280 +-
src/bogart/AS_BAT_SetParentAndHang.H | 2 +
src/bogart/AS_BAT_SplitDiscontinuous.C | 52 +-
src/bogart/AS_BAT_Unitig.C | 505 +++-
src/bogart/AS_BAT_Unitig.H | 280 +-
src/bogart/AS_BAT_UnitigVector.C | 218 ++
src/bogart/AS_BAT_UnitigVector.H | 61 +
src/bogart/AS_BAT_Unitig_AddAndPlaceFrag.C | 144 -
src/bogart/AS_BAT_Unitig_AddFrag.C | 32 +-
src/bogart/AS_BAT_Unitig_PlaceFragUsingEdges.C | 561 +---
src/bogart/AS_BAT_findEdges.C | 178 --
src/bogart/bogart.C | 299 +-
src/bogart/bogart.mk | 13 +-
src/bogart/buildGraph.C | 324 +-
src/correction/errorEstimate.C | 206 ++
src/{mhap/mhap.mk => correction/errorEstimate.mk} | 11 +-
src/falcon_sense/falcon_sense.C | 10 +-
src/falcon_sense/libfalcon/falcon.C | 19 +-
src/falcon_sense/libfalcon/falcon.H | 2 +-
src/falcon_sense/libfalcon/kmer_lookup.C | 0
src/main.mk | 4 +-
src/merTrim/merTrimAdapter.C | 0
src/meryl/libleaff/fastaFile.C | 3 -
src/meryl/libleaff/fastaStdin.C | 14 +-
src/meryl/libleaff/fastqFile.C | 4 -
src/meryl/libleaff/fastqStdin.C | 7 +-
src/meryl/libleaff/gkStoreFile.C | 2 +-
src/meryl/libleaff/seqCache.C | 3 -
src/meryl/libleaff/seqFile.H | 2 +
src/meryl/libmeryl.C | 125 +-
src/meryl/libmeryl.H | 7 +-
src/meryl/meryl-build.C | 65 +-
src/meryl/meryl-dump.C | 4 +-
src/mhap/mhap.mk | 4 +-
.../correctOverlaps-Correct_Frags.C | 13 +-
.../correctOverlaps-Prefix_Edit_Distance.C | 6 +-
.../correctOverlaps-Read_Olaps.C | 7 +
.../correctOverlaps-Redo_Olaps.C | 21 +-
src/overlapErrorAdjustment/correctOverlaps.C | 30 +
src/overlapErrorAdjustment/correctOverlaps.H | 6 +
.../findErrors-Analyze_Alignment.C | 30 +-
src/overlapErrorAdjustment/findErrors-Dump.C | 97 +
.../findErrors-Dump.mk} | 11 +-
src/overlapErrorAdjustment/findErrors.C | 8 +
.../overlapInCore-Process_String_Overlaps.C | 11 +-
src/overlapInCore/overlapInCore.C | 8 +-
src/overlapInCore/overlapInCore.H | 30 +-
src/overlapInCore/overlapPair.C | 27 +-
src/pipelines/bogart-sweep.pl | 185 ++
src/pipelines/canu.pl | 27 +-
src/pipelines/canu/Configure.pm | 118 +-
src/pipelines/canu/CorrectReads.pm | 30 +-
src/pipelines/canu/CorrectReads.txt | 41 +
src/pipelines/canu/Defaults.pm | 118 +-
src/pipelines/canu/ErrorEstimate.pm | 258 ++
src/pipelines/canu/Execution.pm | 103 +-
src/pipelines/canu/Execution.txt | 85 +
src/pipelines/canu/Gatekeeper.pm | 22 +-
src/pipelines/canu/Grid_LSF.pm | 9 +
src/pipelines/canu/Grid_PBSTorque.pm | 33 +-
src/pipelines/canu/Grid_SGE.pm | 11 +
src/pipelines/canu/Grid_Slurm.pm | 43 +-
src/pipelines/canu/HTML.pm | 144 +-
src/pipelines/canu/Meryl.pm | 44 +-
src/pipelines/canu/Output.pm | 8 +-
src/pipelines/canu/OverlapBasedTrimming.pm | 9 +-
src/pipelines/canu/OverlapErrorAdjustment.pm | 59 +-
src/pipelines/canu/OverlapInCore.pm | 13 +
src/pipelines/canu/OverlapMMap.pm | 77 +-
src/pipelines/canu/OverlapMhap.pm | 160 +-
src/pipelines/canu/OverlapStore.pm | 48 +-
src/pipelines/canu/Unitig.pm | 58 +-
src/stores/gatekeeperCreate.C | 6 +-
src/stores/gatekeeperDumpFASTQ.C | 90 +-
src/stores/gkStore.C | 24 +-
src/stores/gkStore.H | 10 +-
src/stores/gkStoreEncode.C | 4 +-
src/stores/ovOverlap.C | 19 +
src/stores/ovStore.H | 6 +
src/stores/ovStoreBuild.C | 103 +-
src/stores/ovStoreDump.C | 389 ++-
src/stores/ovStoreStats.C | 73 +-
src/stores/tgStoreCompress.C | 170 ++
src/{mhap/mhap.mk => stores/tgStoreCompress.mk} | 12 +-
src/stores/tgStoreCoverageStat.C | 66 +-
src/stores/tgStoreLoad.C | 6 +-
src/utgcns/libNDFalcon/dw.C | 0
src/utgcns/libNDFalcon/dw.H | 0
src/utgcns/libcns/NOTES | 38 +
src/utgcns/utgcns.C | 1 +
151 files changed, 9426 insertions(+), 11243 deletions(-)
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