[med-svn] [canu] branch upstream updated (15ffcc1 -> 3dbd24e)
Andreas Tille
tille at debian.org
Sat Sep 2 13:54:57 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository canu.
from 15ffcc1 Imported Upstream version 1.5+dfsg
adds 3dbd24e New upstream version 1.6+dfsg
No new revisions were added by this update.
Summary of changes:
.github/ISSUE_TEMPLATE.md | 21 +
README.citation | 2 +-
README.md | 8 +-
addCopyrights-BuildData.pl | 1 +
addCopyrights.dat | 1020 ++++++++++++++++++++
addCopyrights.pl | 30 +-
buildRelease.sh | 35 +-
documentation/source/conf.py | 4 +-
documentation/source/faq.rst | 63 +-
documentation/source/index.rst | 2 +-
documentation/source/parameter-reference.rst | 39 +-
documentation/source/quick-start.rst | 271 ++----
documentation/source/tutorial.rst | 103 +-
src/AS_UTL/AS_UTL_fileIO.C | 35 +-
src/AS_UTL/AS_UTL_fileIO.H | 1 +
src/AS_UTL/AS_UTL_reverseComplement.C | 129 +--
src/AS_UTL/AS_UTL_reverseComplement.H | 6 +-
src/AS_UTL/bitPackedFile.C | 11 +-
src/AS_UTL/timeAndSize.C | 92 +-
src/AS_UTL/timeAndSize.H | 11 +-
src/AS_UTL/writeBuffer.H | 6 +-
src/AS_global.C | 6 +
src/Makefile | 21 +-
src/bogart/AS_BAT_AssemblyGraph.C | 5 +-
src/bogart/AS_BAT_BestOverlapGraph.C | 27 +-
src/bogart/AS_BAT_BestOverlapGraph.H | 1 +
src/bogart/AS_BAT_CreateUnitigs.C | 553 +++++++++--
src/bogart/AS_BAT_CreateUnitigs.H | 12 +-
src/bogart/AS_BAT_DropDeadEnds.C | 297 ++++++
...AS_BAT_MergeOrphans.H => AS_BAT_DropDeadEnds.H} | 26 +-
src/bogart/AS_BAT_Instrumentation.C | 345 ++++---
src/bogart/AS_BAT_Logging.C | 6 +-
src/bogart/AS_BAT_Logging.H | 2 +-
src/bogart/AS_BAT_MarkRepeatReads.C | 85 +-
src/bogart/AS_BAT_MarkRepeatReads.H | 30 +-
src/bogart/AS_BAT_MergeOrphans.C | 919 ++++++++----------
src/bogart/AS_BAT_OptimizePositions.C | 508 ++++++++++
src/bogart/AS_BAT_Outputs.C | 17 +-
src/bogart/AS_BAT_OverlapCache.C | 644 ++++++------
src/bogart/AS_BAT_OverlapCache.H | 136 ++-
src/bogart/AS_BAT_PlaceContains.C | 4 +-
src/bogart/AS_BAT_PlaceReadUsingOverlaps.C | 647 ++++++-------
src/bogart/AS_BAT_PlaceReadUsingOverlaps.H | 18 +-
src/bogart/AS_BAT_PromoteToSingleton.C | 2 +
src/bogart/AS_BAT_ReadInfo.C | 12 +-
src/bogart/AS_BAT_ReadInfo.H | 16 +-
src/bogart/AS_BAT_SplitDiscontinuous.C | 4 +-
src/bogart/AS_BAT_TigGraph.C | 110 ++-
src/bogart/AS_BAT_TigVector.C | 6 +-
src/bogart/AS_BAT_TigVector.H | 2 +
src/bogart/AS_BAT_Unitig.C | 251 ++---
src/bogart/AS_BAT_Unitig.H | 111 ++-
src/bogart/AS_BAT_Unitig_PlaceReadUsingEdges.C | 30 +-
src/bogart/bogart.C | 282 +++---
src/bogart/bogart.mk | 2 +
src/canu_version_update.pl | 4 +-
src/falcon_sense/falcon_sense.C | 4 +-
src/falcon_sense/libfalcon/falcon.C | 4 +
src/fastq-utilities/fastqSample.C | 8 +-
src/gfa/alignGFA.C | 671 +++++++++++--
src/gfa/bed.C | 173 ++++
src/gfa/{gfa.H => bed.H} | 68 +-
src/gfa/gfa.C | 62 +-
src/gfa/gfa.H | 4 +
src/main.mk | 3 +-
src/meryl/libmeryl.C | 34 +-
src/minimap/mmapConvert.C | 65 +-
src/overlapBasedTrimming/splitReads-trimBad.C | 11 +-
src/overlapBasedTrimming/splitReads-workUnit.C | 8 +-
src/overlapBasedTrimming/splitReads.C | 15 +-
src/overlapErrorAdjustment/findErrors.H | 2 +-
src/overlapInCore/libedlib/edlib.C | 205 ++--
src/overlapInCore/libedlib/edlib.H | 18 +-
src/overlapInCore/liboverlap/Binomial_Bound.C | 8 +
src/overlapInCore/overlapInCorePartition.C | 2 +
src/pipelines/canu.pl | 350 ++++---
src/pipelines/canu/Configure.pm | 127 ++-
src/pipelines/canu/Consensus.pm | 120 ++-
src/pipelines/canu/CorrectReads.pm | 29 +-
src/pipelines/canu/Defaults.pm | 712 +++++++-------
src/pipelines/canu/Execution.pm | 195 ++--
src/pipelines/canu/Gatekeeper.pm | 150 +--
src/pipelines/canu/Grid_LSF.pm | 2 +-
src/pipelines/canu/Grid_PBSTorque.pm | 22 +-
src/pipelines/canu/Meryl.pm | 16 +-
src/pipelines/canu/Output.pm | 7 +
src/pipelines/canu/OverlapBasedTrimming.pm | 3 +-
src/pipelines/canu/OverlapErrorAdjustment.pm | 46 +-
src/pipelines/canu/OverlapInCore.pm | 21 +-
src/pipelines/canu/OverlapMMap.pm | 127 ++-
src/pipelines/canu/OverlapMhap.pm | 43 +-
src/pipelines/canu/OverlapStore.pm | 214 ++--
src/pipelines/canu/Unitig.pm | 20 +-
src/stores/gatekeeperPartition.C | 77 +-
src/stores/gkStore.C | 16 +-
src/stores/ovStoreBucketizer.C | 2 +
src/stores/ovStoreDump.C | 18 +-
src/stores/ovStoreIndexer.C | 2 +-
src/stores/ovStoreSorter.C | 39 +-
src/stores/ovStoreWriter.C | 10 +-
src/stores/tgStore.C | 8 +-
src/stores/tgTig.C | 6 +-
src/utgcns/libNDFalcon/LICENSE | 36 -
src/utgcns/libNDFalcon/dw.C | 359 -------
src/utgcns/libNDFalcon/dw.H | 161 ---
src/utgcns/libcns/unitigConsensus.C | 752 ++++++++++-----
src/utgcns/libcns/unitigConsensus.H | 7 +-
src/utgcns/libpbutgcns/Alignment.C | 113 ---
src/utgcns/libpbutgcns/Alignment.H | 65 +-
src/utgcns/libpbutgcns/AlnGraphBoost.C | 8 +-
src/utgcns/libpbutgcns/AlnGraphBoost.H | 6 +-
src/utgcns/utgcns.C | 185 ++--
112 files changed, 8012 insertions(+), 4458 deletions(-)
create mode 100644 .github/ISSUE_TEMPLATE.md
create mode 100644 src/bogart/AS_BAT_DropDeadEnds.C
copy src/bogart/{AS_BAT_MergeOrphans.H => AS_BAT_DropDeadEnds.H} (70%)
create mode 100644 src/bogart/AS_BAT_OptimizePositions.C
create mode 100644 src/gfa/bed.C
copy src/gfa/{gfa.H => bed.H} (58%)
delete mode 100644 src/utgcns/libNDFalcon/LICENSE
delete mode 100644 src/utgcns/libNDFalcon/dw.C
delete mode 100644 src/utgcns/libNDFalcon/dw.H
delete mode 100644 src/utgcns/libpbutgcns/Alignment.C
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