[med-svn] [canu] branch upstream updated (71abef9 -> 15ffcc1)
Afif Elghraoui
afif at moszumanska.debian.org
Thu May 18 05:30:14 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 71abef9 Imported Upstream version 1.4+dfsg
new 15ffcc1 Imported Upstream version 1.5+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.licenses | 43 +
addCopyrights-BuildData.pl | 1 +
addCopyrights.dat | 729 +++++
addCopyrights.pl | 41 +-
buildRelease.sh | 39 +
documentation/reST-markup-hints | 10 +
documentation/source/conf.py | 4 +-
documentation/source/faq.rst | 95 +-
documentation/source/parameter-reference.rst | 418 ++-
documentation/source/quick-start.rst | 55 +-
documentation/source/tutorial.rst | 114 +-
src/AS_UTL/AS_UTL_fileIO.C | 149 +-
src/AS_UTL/AS_UTL_fileIO.H | 8 +-
src/AS_UTL/AS_UTL_stackTrace.C | 376 ++-
src/AS_UTL/AS_UTL_stackTrace.H | 2 +-
src/AS_UTL/bitPackedFile.C | 2 +-
src/AS_UTL/libbacktrace/LICENSE | 29 +
src/AS_UTL/libbacktrace/README | 15 +
src/AS_UTL/libbacktrace/atomic.c | 113 +
src/AS_UTL/libbacktrace/backtrace-supported.h | 66 +
src/AS_UTL/libbacktrace/backtrace.c | 129 +
src/AS_UTL/libbacktrace/backtrace.h | 182 ++
src/AS_UTL/libbacktrace/config.h | 128 +
src/AS_UTL/libbacktrace/dwarf.c | 3123 ++++++++++++++++++++
src/AS_UTL/libbacktrace/elf.c | 983 ++++++
src/AS_UTL/libbacktrace/fileline.c | 194 ++
src/AS_UTL/libbacktrace/internal.h | 294 ++
src/AS_UTL/libbacktrace/make.out | 26 +
src/AS_UTL/libbacktrace/make.sh | 22 +
src/AS_UTL/libbacktrace/mmap.c | 303 ++
src/AS_UTL/libbacktrace/mmapio.c | 100 +
src/AS_UTL/libbacktrace/posix.c | 100 +
src/AS_UTL/libbacktrace/print.c | 92 +
src/AS_UTL/libbacktrace/simple.c | 108 +
src/AS_UTL/libbacktrace/sort.c | 108 +
src/AS_UTL/libbacktrace/state.c | 72 +
src/AS_UTL/libbacktrace/unknown.c | 68 +
src/AS_global.C | 9 +-
src/Makefile | 227 +-
src/bogart/AS_BAT_BestOverlapGraph.C | 90 +-
src/bogart/AS_BAT_BestOverlapGraph.H | 10 +-
src/bogart/AS_BAT_ChunkGraph.C | 16 +-
src/bogart/AS_BAT_CreateUnitigs.C | 2 +-
src/bogart/AS_BAT_MergeOrphans.H | 6 +-
src/bogart/AS_BAT_OverlapCache.C | 70 +-
src/bogart/AS_BAT_TigGraph.C | 28 +-
src/bogart/bogart.C | 25 +-
src/canu_version_update.pl | 58 +-
src/correction/generateCorrectionLayouts.C | 63 +-
src/falcon_sense/falcon_sense.C | 21 +
src/falcon_sense/falcon_sense.mk | 2 +-
src/falcon_sense/libfalcon/falcon.C | 240 +-
src/falcon_sense/libfalcon/falcon.H | 75 +-
src/falcon_sense/libfalcon/kmer_lookup.C | 622 ----
src/fastq-utilities/fastqSimulate.C | 4 +-
src/gfa/alignGFA.C | 464 +++
.../gatekeeperCreate.mk => gfa/alignGFA.mk} | 7 +-
src/gfa/gfa.C | 345 +++
src/gfa/gfa.H | 103 +
src/main.mk | 43 +-
src/merTrim/merTrim.C | 183 +-
.../merTrim.mk} | 8 +-
src/merTrim/merTrimResult.H | 9 +-
src/meryl/compare-counts.C | 4 +
src/meryl/estimate-mer-threshold.C | 310 +-
src/meryl/existDB.C | 252 ++
src/meryl/{maskMers.mk => existDB.mk} | 6 +-
src/meryl/libkmer/existDB-create-from-fasta.C | 304 ++
src/meryl/libkmer/existDB-create-from-meryl.C | 261 ++
src/meryl/libkmer/existDB-create-from-sequence.C | 293 ++
src/meryl/libkmer/existDB-state.C | 233 ++
src/meryl/libkmer/existDB.C | 211 ++
src/meryl/libkmer/existDB.H | 190 ++
src/meryl/libkmer/existDB.mk | 13 +
src/meryl/libkmer/percentCovered.C | 95 +
src/meryl/libkmer/percentCovered.mk | 13 +
src/meryl/libkmer/posDB.mk | 13 +
src/meryl/libkmer/positionDB-access.C | 376 +++
src/meryl/libkmer/positionDB-dump.C | 79 +
src/meryl/libkmer/positionDB-file.C | 318 ++
src/meryl/libkmer/positionDB-mismatch.C | 412 +++
src/meryl/libkmer/positionDB-sort.C | 182 ++
src/meryl/libkmer/positionDB.C | 1186 ++++++++
src/meryl/libkmer/positionDB.H | 273 ++
src/meryl/maskMers.C | 4 +
src/meryl/meryl-build.C | 20 +
src/meryl/positionDB.C | 308 ++
src/meryl/{maskMers.mk => positionDB.mk} | 6 +-
src/mhap/mhapConvert.C | 33 +-
src/minimap/mmapConvert.C | 36 +-
src/overlapInCore/libedlib/edlib.C | 65 +-
src/overlapInCore/libedlib/edlib.H | 327 +-
.../prefixEditDistance-allocateMoreSpace.C | 13 +-
.../liboverlap/prefixEditDistance-extend.C | 18 +-
.../liboverlap/prefixEditDistance-forward.C | 36 +-
.../liboverlap/prefixEditDistance-reverse.C | 36 +-
src/overlapInCore/liboverlap/prefixEditDistance.H | 21 +-
.../overlapInCore-Process_String_Overlaps.C | 2 +-
src/overlapInCore/overlapPair.C | 710 +++--
src/pipelines/canu-object-store.pl | 152 +
src/pipelines/canu.pl | 405 +--
src/pipelines/canu/Configure.pm | 193 +-
src/pipelines/canu/Consensus.pm | 465 ++-
src/pipelines/canu/CorrectReads.pm | 688 +++--
src/pipelines/canu/Defaults.pm | 407 ++-
src/pipelines/canu/ErrorEstimate.pm | 102 +-
src/pipelines/canu/Execution.pm | 508 +++-
src/pipelines/canu/Gatekeeper.pm | 369 +--
src/pipelines/canu/Grid_Cloud.pm | 347 +++
src/pipelines/canu/Grid_DNANexus.pm | 104 +
src/pipelines/canu/Grid_LSF.pm | 3 -
src/pipelines/canu/Grid_PBSTorque.pm | 19 +-
src/pipelines/canu/Grid_SGE.pm | 34 +-
src/pipelines/canu/Grid_Slurm.pm | 3 -
src/pipelines/canu/HTML.pm | 214 +-
src/pipelines/canu/Meryl.pm | 573 ++--
src/pipelines/canu/Output.pm | 150 +-
src/pipelines/canu/OverlapBasedTrimming.pm | 165 +-
src/pipelines/canu/OverlapErrorAdjustment.pm | 345 ++-
src/pipelines/canu/OverlapInCore.pm | 216 +-
src/pipelines/canu/OverlapMMap.pm | 298 +-
src/pipelines/canu/OverlapMhap.pm | 352 ++-
src/pipelines/canu/OverlapStore.pm | 428 +--
src/pipelines/canu/Report.pm | 172 ++
src/pipelines/canu/Unitig.pm | 169 +-
src/pipelines/parallel-ovl-store-test.sh | 68 +
src/pipelines/sanity/sanity-all-done.pl | 240 --
src/pipelines/sanity/sanity-merge-qc.pl | 121 -
src/pipelines/sanity/sanity.pl | 382 ---
src/pipelines/sanity/sanity.sh | 50 -
src/pipelines/simple-repeat-test.pl | 107 +
src/stores/gatekeeperPartition.C | 82 +-
src/stores/gkStore.C | 35 +-
src/stores/gkStore.H | 3 +-
src/stores/ovOverlap.C | 13 +-
src/stores/ovOverlap.H | 18 +-
src/stores/ovStore.C | 115 +-
src/stores/ovStore.H | 10 +-
src/stores/ovStoreBucketizer.C | 4 +-
src/stores/ovStoreBuild.C | 13 +-
src/stores/ovStoreFile.C | 202 +-
src/stores/ovStoreFilter.C | 23 +-
src/stores/ovStoreHistogram.C | 28 +-
src/stores/ovStoreHistogram.H | 4 +-
src/stores/ovStoreWriter.C | 12 +-
src/stores/tgStore.C | 8 +-
src/stores/tgStoreCoverageStat.C | 4 +-
src/stores/tgStoreDump.C | 16 +-
src/stores/tgStoreLoad.C | 41 +-
src/stores/tgTig.C | 32 +
src/stores/tgTig.H | 2 +
src/stores/tgTigMultiAlignDisplay.C | 2 +-
src/utgcns/libNDFalcon/dw.C | 10 +
src/utgcns/libcns/unitigConsensus.C | 134 +-
src/utgcns/libcns/unitigConsensus.H | 3 +-
src/utgcns/libpbutgcns/LICENSE | 72 +-
src/utgcns/utgcns.C | 5 +-
157 files changed, 20626 insertions(+), 5844 deletions(-)
create mode 100644 buildRelease.sh
create mode 100644 documentation/reST-markup-hints
create mode 100644 src/AS_UTL/libbacktrace/LICENSE
create mode 100644 src/AS_UTL/libbacktrace/README
create mode 100644 src/AS_UTL/libbacktrace/atomic.c
create mode 100644 src/AS_UTL/libbacktrace/backtrace-supported.h
create mode 100644 src/AS_UTL/libbacktrace/backtrace.c
create mode 100644 src/AS_UTL/libbacktrace/backtrace.h
create mode 100644 src/AS_UTL/libbacktrace/config.h
create mode 100644 src/AS_UTL/libbacktrace/dwarf.c
create mode 100644 src/AS_UTL/libbacktrace/elf.c
create mode 100644 src/AS_UTL/libbacktrace/fileline.c
create mode 100644 src/AS_UTL/libbacktrace/internal.h
create mode 100644 src/AS_UTL/libbacktrace/make.out
create mode 100644 src/AS_UTL/libbacktrace/make.sh
create mode 100644 src/AS_UTL/libbacktrace/mmap.c
create mode 100644 src/AS_UTL/libbacktrace/mmapio.c
create mode 100644 src/AS_UTL/libbacktrace/posix.c
create mode 100644 src/AS_UTL/libbacktrace/print.c
create mode 100644 src/AS_UTL/libbacktrace/simple.c
create mode 100644 src/AS_UTL/libbacktrace/sort.c
create mode 100644 src/AS_UTL/libbacktrace/state.c
create mode 100644 src/AS_UTL/libbacktrace/unknown.c
delete mode 100644 src/falcon_sense/libfalcon/kmer_lookup.C
create mode 100644 src/gfa/alignGFA.C
copy src/{stores/gatekeeperCreate.mk => gfa/alignGFA.mk} (78%)
create mode 100644 src/gfa/gfa.C
create mode 100644 src/gfa/gfa.H
copy src/{meryl/estimate-mer-threshold.mk => merTrim/merTrim.mk} (76%)
create mode 100644 src/meryl/existDB.C
copy src/meryl/{maskMers.mk => existDB.mk} (82%)
create mode 100644 src/meryl/libkmer/existDB-create-from-fasta.C
create mode 100644 src/meryl/libkmer/existDB-create-from-meryl.C
create mode 100644 src/meryl/libkmer/existDB-create-from-sequence.C
create mode 100644 src/meryl/libkmer/existDB-state.C
create mode 100644 src/meryl/libkmer/existDB.C
create mode 100644 src/meryl/libkmer/existDB.H
create mode 100644 src/meryl/libkmer/existDB.mk
create mode 100644 src/meryl/libkmer/percentCovered.C
create mode 100644 src/meryl/libkmer/percentCovered.mk
create mode 100644 src/meryl/libkmer/posDB.mk
create mode 100644 src/meryl/libkmer/positionDB-access.C
create mode 100644 src/meryl/libkmer/positionDB-dump.C
create mode 100644 src/meryl/libkmer/positionDB-file.C
create mode 100644 src/meryl/libkmer/positionDB-mismatch.C
create mode 100644 src/meryl/libkmer/positionDB-sort.C
create mode 100644 src/meryl/libkmer/positionDB.C
create mode 100644 src/meryl/libkmer/positionDB.H
create mode 100644 src/meryl/positionDB.C
copy src/meryl/{maskMers.mk => positionDB.mk} (81%)
create mode 100755 src/pipelines/canu-object-store.pl
create mode 100644 src/pipelines/canu/Grid_Cloud.pm
create mode 100644 src/pipelines/canu/Grid_DNANexus.pm
create mode 100644 src/pipelines/canu/Report.pm
create mode 100644 src/pipelines/parallel-ovl-store-test.sh
delete mode 100644 src/pipelines/sanity/sanity-all-done.pl
delete mode 100644 src/pipelines/sanity/sanity-merge-qc.pl
delete mode 100755 src/pipelines/sanity/sanity.pl
delete mode 100644 src/pipelines/sanity/sanity.sh
create mode 100644 src/pipelines/simple-repeat-test.pl
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