[med-svn] [bedtools] branch master updated (86c9cf2 -> 69e2731)
Charles Plessy
plessy at moszumanska.debian.org
Fri Sep 19 01:02:19 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository bedtools.
from 86c9cf2 Merge branch 'master' of ssh://git.debian.org/git/debian-med/bedtools
new ccd125c Added new -iobuf option and unit tests.
new 6f0be00 Merge pull request #86 from nkindlon/master
new 80488b8 adjust Makefile to accomodate Intel compiler.
new 699172f Update links in docs to point to the bedtools2 github pages.
new b877b35 Merge pull request #89 from mdshw5/master
new 5fc981c Move "using namespace std" after #includes
new ed64d68 Miscellaneous portability / warning fixes
new b84b182 Check stderr is empty, not stdout (fixes test for #46)
new 9e63df9 Merge pull request #95 from jmarshall/warnings2
new fef96d4 Merge branch 'master' of https://github.com/arq5x/bedtools2
new 762deee Fisher's Exact Test
new 1b311e8 Merge pull request #94 from brentp/stats
new 9249816 add @brentp's fisher tool to the help menu.
new ecb4afa fix slop with -pct
new b22d89e make sure it doesn't accumulate
new bc2f97d Merge pull request #99 from brentp/sloppy
new 80035a6 Update overview.rst
new 24bde2d Merge pull request #108 from bioinfocoderz/patch-1
new d1b0d0d Add human hg38 genome file
new aa6dcea Merge pull request #107 from martijnvermaat/hg38
new 2f6f6cf Update the format on code block
new 9b17893 Merge pull request #110 from dhoeric/patch-1
new cb06202 Update intersect.rst
new dfabf63 Merge pull request #111 from hiberbear/patch-1
new a4647ea Allow compilation with FreeBSD/clang.
new 966522a Merge pull request #112 from cinquin/master
new 56761cd Changes for multi-DB intersection.
new 509cc91 Multiple DB intersect support with unit tests and updated help messages.
new 7f0b3f5 First check-in for multi-sweep
new f581e4d Corrected merge conflicts
new 57ed945 Corrected errors caused during merge-conflict resolution
new 653dc11 merge conflict corrections
new 7bea854 fixing merge errors, again.
new 7434d8a Stop Chromsweeep cache scan when DB is after query; allow BAM unmapped reads/chrom in genome file.
new 130cba7 fix merge conflicts
new 3dff8ca [DOC] remove sticky note from docs. general hatred.
new 89cf3bc update fisher to use RecordKeyVector
new 746cca4 logo:
new 0048bd2 update release history
new 04ee93b update docs and figures for multi-db intersect
new 4356ace Setting Release-Version v2.21.0
new 2aa53ad [DOC] typo
new 6a92b11 latest=2.21.0
new 69e2731 Merge branch 'master' of https://github.com/arq5x/bedtools2
The 44 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:
Makefile | 5 +-
README.md | 2 +-
RELEASE_HISTORY | 86 +++-
docs/_static/labibi.css | 9 -
docs/bedtools.swiss.png | Bin 0 -> 8133 bytes
docs/conf.py | 6 +-
docs/content/bedtools-suite.rst | 3 +-
docs/content/history.rst | 12 +
.../content/images/tool-glyphs/intersect-glyph.png | Bin 34437 -> 94521 bytes
docs/content/installation.rst | 48 +--
docs/content/overview.rst | 2 +-
docs/content/tools/coverage.rst | 9 +-
docs/content/tools/fisher.rst | 119 ++++++
docs/content/tools/intersect.rst | 222 +++++++++-
docs/templates/page.html | 7 +-
docs/templates/sidebar-intro.html | 11 +-
genomes/human.hg38.genome | 455 +++++++++++++++++++++
src/bedtools.cpp | 3 +
src/fisher/Fisher.cpp | 112 +++++
src/fisher/Fisher.h | 30 ++
src/{jaccard => fisher}/Makefile | 9 +-
src/fisher/fisherMain.cpp | 72 ++++
src/fisher/kfunc.c | 253 ++++++++++++
src/intersectFile/intersectFile.cpp | 14 +-
src/intersectFile/intersectFile.h | 6 +-
src/intersectFile/intersectMain.cpp | 18 +-
src/jaccard/Jaccard.cpp | 12 +-
src/jaccard/Jaccard.h | 2 +-
src/mapFile/mapFile.cpp | 6 +-
src/mapFile/mapFile.h | 4 +-
src/mapFile/mapMain.cpp | 3 +-
src/mergeFile/mergeFile.cpp | 2 +-
src/nekSandbox1/nekSandboxMain.cpp | 2 -
src/regressTest/RegressTest.h | 5 +-
src/sampleFile/SampleFile.h | 4 +-
src/slopBed/slopBed.cpp | 8 +-
src/subtractBed/subtractBed.cpp | 2 +-
.../BamTools/src/api/internal/io/HostInfo_p.cpp | 3 +
.../src/api/internal/io/TcpSocketEngine_unix_p.cpp | 4 +-
src/utils/BinTree/BinTree.cpp | 38 +-
src/utils/BinTree/BinTree.h | 11 +-
src/utils/Contexts/ContextBase.cpp | 99 ++++-
src/utils/Contexts/ContextBase.h | 51 +--
.../{ContextJaccard.cpp => ContextFisher.cpp} | 32 +-
.../Contexts/{ContextJaccard.h => ContextFisher.h} | 15 +-
src/utils/Contexts/ContextIntersect.cpp | 58 ++-
src/utils/Contexts/ContextIntersect.h | 18 +-
src/utils/Contexts/ContextMap.cpp | 14 +
src/utils/Contexts/ContextMap.h | 2 +
src/utils/Contexts/Makefile | 7 +-
src/utils/Fasta/Fasta.cpp | 6 +-
.../FileRecordTools/FileReaders/BamFileReader.h | 2 -
.../FileReaders/BufferedStreamMgr.cpp | 4 +-
.../FileReaders/BufferedStreamMgr.h | 7 +-
.../FileRecordTools/FileReaders/FileReader.cpp | 2 +-
src/utils/FileRecordTools/FileReaders/FileReader.h | 8 +-
.../FileRecordTools/FileReaders/InputStreamMgr.h | 4 +-
src/utils/FileRecordTools/FileReaders/Makefile | 6 +-
.../FileReaders/{Makefile => Makefile~} | 0
.../FileReaders/SingleLineDelimTextFileReader.h | 2 -
.../FileReaders/SingleLineDelimTransferBuffer.cpp | 2 +
.../FileReaders/SingleLineDelimTransferBuffer.h | 2 -
src/utils/FileRecordTools/FileRecordMergeMgr.cpp | 16 +-
src/utils/FileRecordTools/FileRecordMergeMgr.h | 8 +-
src/utils/FileRecordTools/FileRecordMgr.cpp | 11 +-
src/utils/FileRecordTools/FileRecordMgr.h | 18 +-
src/utils/FileRecordTools/Records/BamRecord.cpp | 15 +-
src/utils/FileRecordTools/Records/BamRecord.h | 10 +-
src/utils/FileRecordTools/Records/Bed3Interval.cpp | 1 +
src/utils/FileRecordTools/Records/BlockMgr.cpp | 38 +-
src/utils/FileRecordTools/Records/BlockMgr.h | 19 +-
src/utils/FileRecordTools/Records/GffRecord.cpp | 1 +
src/utils/FileRecordTools/Records/Makefile | 14 +-
src/utils/FileRecordTools/Records/Record.cpp | 34 +-
src/utils/FileRecordTools/Records/Record.h | 19 +-
src/utils/FileRecordTools/Records/RecordKeyList.h | 13 +-
.../FileRecordTools/Records/RecordKeyVector.cpp | 88 ++++
.../FileRecordTools/Records/RecordKeyVector.h | 62 +++
src/utils/FileRecordTools/Records/RecordList.cpp | 202 +++++++++
src/utils/FileRecordTools/Records/RecordList.h | 117 ++++++
src/utils/FileRecordTools/Records/StrandQueue.h | 6 +-
src/utils/FileRecordTools/Records/VcfRecord.cpp | 5 +-
src/utils/GenomeFile/NewGenomeFile.cpp | 17 +-
src/utils/GenomeFile/NewGenomeFile.h | 2 +-
src/utils/KeyListOps/KeyListOps.cpp | 2 +-
src/utils/KeyListOps/KeyListOps.h | 4 +-
src/utils/KeyListOps/KeyListOpsMethods.cpp | 6 +-
src/utils/KeyListOps/KeyListOpsMethods.h | 16 +-
src/utils/NewChromsweep/NewChromsweep.cpp | 221 ++++++----
src/utils/NewChromsweep/NewChromsweep.h | 63 +--
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 34 +-
src/utils/RecordOutputMgr/RecordOutputMgr.h | 17 +-
src/utils/fileType/FileRecordTypeChecker.cpp | 1 +
src/utils/fileType/FileRecordTypeChecker.h | 6 +-
src/utils/general/CommonHelp.cpp | 17 +
src/utils/general/CommonHelp.h | 19 +
src/utils/general/CompressionTools.h | 2 -
src/utils/general/FreeList.h | 4 +-
src/utils/general/Makefile | 7 +-
src/utils/general/ParseTools.h | 4 +-
src/utils/general/PushBackStreamBuf.h | 6 +-
src/utils/general/QuickString.cpp | 5 +
src/utils/general/QuickString.h | 4 +-
src/utils/general/Tokenizer.h | 4 +-
src/utils/version/version_release.txt | 6 +-
test/general/test-general.sh | 2 +-
test/intersect/multi_intersect/d1.bed | 9 +
test/intersect/multi_intersect/d2.bed | 6 +
test/intersect/multi_intersect/d3.bed | 3 +
test/intersect/multi_intersect/d4.bed | 9 +
test/intersect/multi_intersect/d5.bed | 6 +
test/intersect/multi_intersect/d6.bed | 3 +
test/intersect/multi_intersect/d7.bed | 10 +
test/intersect/multi_intersect/d8.bed | 7 +
test/intersect/multi_intersect/d9.bed | 4 +
test/intersect/multi_intersect/g.bed | 3 +
test/intersect/multi_intersect/query.bed | 12 +
test/intersect/multi_intersect/query2.bed | 13 +
test/intersect/multi_intersect/query3.bed | 13 +
.../multi_intersect/test-multi_intersect.sh | 404 ++++++++++++++++++
...ew_test-intersect.sh => new_test-intersect.sh~} | 2 +-
test/intersect/performanceTest.sh | 2 +-
test/intersect/test-intersect.sh | 7 +-
test/merge/test-merge.sh | 69 ++++
test/slop/test-slop.sh | 8 +-
125 files changed, 3220 insertions(+), 496 deletions(-)
create mode 100644 docs/bedtools.swiss.png
create mode 100644 docs/content/tools/fisher.rst
create mode 100644 genomes/human.hg38.genome
create mode 100644 src/fisher/Fisher.cpp
create mode 100644 src/fisher/Fisher.h
copy src/{jaccard => fisher}/Makefile (89%)
create mode 100644 src/fisher/fisherMain.cpp
create mode 100644 src/fisher/kfunc.c
copy src/utils/Contexts/{ContextJaccard.cpp => ContextFisher.cpp} (81%)
copy src/utils/Contexts/{ContextJaccard.h => ContextFisher.h} (54%)
copy src/utils/FileRecordTools/FileReaders/{Makefile => Makefile~} (100%)
create mode 100644 src/utils/FileRecordTools/Records/RecordKeyVector.cpp
create mode 100644 src/utils/FileRecordTools/Records/RecordKeyVector.h
create mode 100644 src/utils/FileRecordTools/Records/RecordList.cpp
create mode 100644 src/utils/FileRecordTools/Records/RecordList.h
create mode 100644 src/utils/general/CommonHelp.cpp
create mode 100644 src/utils/general/CommonHelp.h
create mode 100644 test/intersect/multi_intersect/d1.bed
create mode 100644 test/intersect/multi_intersect/d2.bed
create mode 100644 test/intersect/multi_intersect/d3.bed
create mode 100644 test/intersect/multi_intersect/d4.bed
create mode 100644 test/intersect/multi_intersect/d5.bed
create mode 100644 test/intersect/multi_intersect/d6.bed
create mode 100644 test/intersect/multi_intersect/d7.bed
create mode 100644 test/intersect/multi_intersect/d8.bed
create mode 100644 test/intersect/multi_intersect/d9.bed
create mode 100644 test/intersect/multi_intersect/g.bed
create mode 100644 test/intersect/multi_intersect/query.bed
create mode 100644 test/intersect/multi_intersect/query2.bed
create mode 100644 test/intersect/multi_intersect/query3.bed
create mode 100644 test/intersect/multi_intersect/test-multi_intersect.sh
copy test/intersect/{new_test-intersect.sh => new_test-intersect.sh~} (99%)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bedtools.git
More information about the debian-med-commit
mailing list