[med-svn] [bedtools] branch debian/unstable updated (08063ad -> a4f6ab7)
Charles Plessy
plessy at moszumanska.debian.org
Fri Sep 19 01:06:11 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch debian/unstable
in repository bedtools.
from 08063ad Merge branch 'debian/unstable' of ssh://git.debian.org/git/debian-med/bedtools into debian/unstable
adds ccd125c Added new -iobuf option and unit tests.
adds 6f0be00 Merge pull request #86 from nkindlon/master
adds 80488b8 adjust Makefile to accomodate Intel compiler.
adds 699172f Update links in docs to point to the bedtools2 github pages.
adds b877b35 Merge pull request #89 from mdshw5/master
adds 5fc981c Move "using namespace std" after #includes
adds ed64d68 Miscellaneous portability / warning fixes
adds b84b182 Check stderr is empty, not stdout (fixes test for #46)
adds 9e63df9 Merge pull request #95 from jmarshall/warnings2
adds fef96d4 Merge branch 'master' of https://github.com/arq5x/bedtools2
adds 762deee Fisher's Exact Test
adds 1b311e8 Merge pull request #94 from brentp/stats
adds 9249816 add @brentp's fisher tool to the help menu.
adds ecb4afa fix slop with -pct
adds b22d89e make sure it doesn't accumulate
adds bc2f97d Merge pull request #99 from brentp/sloppy
adds 80035a6 Update overview.rst
adds 24bde2d Merge pull request #108 from bioinfocoderz/patch-1
adds d1b0d0d Add human hg38 genome file
adds aa6dcea Merge pull request #107 from martijnvermaat/hg38
adds 2f6f6cf Update the format on code block
adds 9b17893 Merge pull request #110 from dhoeric/patch-1
adds cb06202 Update intersect.rst
adds dfabf63 Merge pull request #111 from hiberbear/patch-1
adds a4647ea Allow compilation with FreeBSD/clang.
adds 966522a Merge pull request #112 from cinquin/master
adds 56761cd Changes for multi-DB intersection.
adds 509cc91 Multiple DB intersect support with unit tests and updated help messages.
adds 7f0b3f5 First check-in for multi-sweep
adds f581e4d Corrected merge conflicts
adds 57ed945 Corrected errors caused during merge-conflict resolution
adds 653dc11 merge conflict corrections
adds 7bea854 fixing merge errors, again.
adds 7434d8a Stop Chromsweeep cache scan when DB is after query; allow BAM unmapped reads/chrom in genome file.
adds 130cba7 fix merge conflicts
adds 3dff8ca [DOC] remove sticky note from docs. general hatred.
adds 89cf3bc update fisher to use RecordKeyVector
adds 746cca4 logo:
adds 0048bd2 update release history
adds 04ee93b update docs and figures for multi-db intersect
adds 4356ace Setting Release-Version v2.21.0
new 856a5fd Merge tag 'v2.21.0' into debian/unstable
adds 86c9cf2 Merge branch 'master' of ssh://git.debian.org/git/debian-med/bedtools
adds 2aa53ad [DOC] typo
adds 6a92b11 latest=2.21.0
adds 69e2731 Merge branch 'master' of https://github.com/arq5x/bedtools2
new a4f6ab7 Merge branch 'master' into debian/unstable
The 2 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%)
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