[med-svn] [canu] branch master updated (503d633 -> f9dd250)
Afif Elghraoui
afif at moszumanska.debian.org
Wed Jul 13 15:49:17 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch master
in repository canu.
from 503d633 Check-in the d/install file
new 7ec4c5f Check-in patch to find private executables
new bce57ac Imported Upstream version 1.3+dfsg
new 5661d4f Merge tag 'upstream/1.3+dfsg'
new b7ddae3 Bump changelog version
new 6a76a51 Update patch
new f9dd250 Bump minimum required mhap version
The 6 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.md | 32 +-
addCopyrights-BuildData.pl | 10 +-
addCopyrights.dat | 3119 +++-----------------
addCopyrights.pl | 2 +-
debian/changelog | 2 +-
debian/control | 2 +-
debian/patches/relative-paths.patch | 15 +
debian/patches/series | 1 +
debian/patches/use-debian-mhap-at-runtime.patch | 23 +-
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 +-
.../Binomial_Bound.H => AS_UTL/intervalListTest.C} | 47 +-
src/AS_UTL/memoryMappedFile.H | 8 +-
src/AS_UTL/stddev.C | 41 -
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_IntersectBubble.H | 44 -
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_Joining.H | 45 -
src/bogart/AS_BAT_Logging.C | 76 +-
src/bogart/AS_BAT_Logging.H | 17 +-
src/bogart/AS_BAT_MarkRepeatReads.C | 1133 +++++++
.../AS_BAT_MarkRepeatReads.H} | 20 +-
src/bogart/AS_BAT_MergeSplitJoin.C | 1763 -----------
src/bogart/AS_BAT_MergeSplitJoin.H | 57 -
src/bogart/AS_BAT_MergeUnitigs.C | 246 ++
.../AS_BAT_MergeUnitigs.H} | 18 +-
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_PlaceZombies.H | 44 -
src/bogart/AS_BAT_PopBubbles.C | 679 +++++
.../SimpleAligner.H => bogart/AS_BAT_PopBubbles.H} | 21 +-
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} | 20 +-
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 ++
.../{readConsensus.mk => errorEstimate.mk} | 4 +-
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} | 6 +-
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 ++
.../{ovStoreSorter.mk => tgStoreCompress.mk} | 4 +-
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 +
160 files changed, 9439 insertions(+), 11401 deletions(-)
create mode 100644 debian/patches/relative-paths.patch
create mode 100644 documentation/source/faq.rst
copy src/{overlapInCore/liboverlap/Binomial_Bound.H => AS_UTL/intervalListTest.C} (51%)
delete mode 100644 src/AS_UTL/stddev.C
create mode 100644 src/AS_UTL/stddevTest.C
delete mode 100644 src/bogart/AS_BAT_Breaking.C
delete mode 100644 src/bogart/AS_BAT_Breaking.H
delete mode 100644 src/bogart/AS_BAT_Datatypes.H
create mode 100644 src/bogart/AS_BAT_FragmentInfo.H
delete mode 100644 src/bogart/AS_BAT_IntersectBubble.C
delete mode 100644 src/bogart/AS_BAT_IntersectBubble.H
delete mode 100644 src/bogart/AS_BAT_IntersectSplit.C
delete mode 100644 src/bogart/AS_BAT_IntersectSplit.H
delete mode 100644 src/bogart/AS_BAT_Joining.C
delete mode 100644 src/bogart/AS_BAT_Joining.H
create mode 100644 src/bogart/AS_BAT_MarkRepeatReads.C
copy src/{utgcns/libpbutgcns/SimpleAligner.H => bogart/AS_BAT_MarkRepeatReads.H} (70%)
delete mode 100644 src/bogart/AS_BAT_MergeSplitJoin.C
delete mode 100644 src/bogart/AS_BAT_MergeSplitJoin.H
create mode 100644 src/bogart/AS_BAT_MergeUnitigs.C
copy src/{utgcns/libpbutgcns/SimpleAligner.H => bogart/AS_BAT_MergeUnitigs.H} (74%)
delete mode 100644 src/bogart/AS_BAT_PlaceZombies.C
delete mode 100644 src/bogart/AS_BAT_PlaceZombies.H
create mode 100644 src/bogart/AS_BAT_PopBubbles.C
copy src/{utgcns/libpbutgcns/SimpleAligner.H => bogart/AS_BAT_PopBubbles.H} (72%)
create mode 100644 src/bogart/AS_BAT_PopBubbles.txt
copy src/{utgcns/libpbutgcns/SimpleAligner.H => bogart/AS_BAT_PromoteToSingleton.H} (75%)
delete mode 100644 src/bogart/AS_BAT_RepeatJunctionEvidence.H
create mode 100644 src/bogart/AS_BAT_UnitigVector.C
create mode 100644 src/bogart/AS_BAT_UnitigVector.H
delete mode 100644 src/bogart/AS_BAT_Unitig_AddAndPlaceFrag.C
delete mode 100644 src/bogart/AS_BAT_findEdges.C
create mode 100644 src/correction/errorEstimate.C
copy src/correction/{readConsensus.mk => errorEstimate.mk} (90%)
mode change 100755 => 100644 src/falcon_sense/libfalcon/falcon.C
mode change 100755 => 100644 src/falcon_sense/libfalcon/falcon.H
mode change 100755 => 100644 src/falcon_sense/libfalcon/kmer_lookup.C
mode change 100755 => 100644 src/merTrim/merTrimAdapter.C
create mode 100644 src/overlapErrorAdjustment/findErrors-Dump.C
copy src/{bogus/bogusness.mk => overlapErrorAdjustment/findErrors-Dump.mk} (75%)
create mode 100644 src/pipelines/bogart-sweep.pl
create mode 100644 src/pipelines/canu/CorrectReads.txt
create mode 100644 src/pipelines/canu/ErrorEstimate.pm
create mode 100644 src/pipelines/canu/Execution.txt
create mode 100644 src/stores/tgStoreCompress.C
copy src/stores/{ovStoreSorter.mk => tgStoreCompress.mk} (87%)
mode change 100755 => 100644 src/utgcns/libNDFalcon/dw.C
mode change 100755 => 100644 src/utgcns/libNDFalcon/dw.H
create mode 100644 src/utgcns/libcns/NOTES
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/canu.git
More information about the debian-med-commit
mailing list