[med-svn] [bedtools] branch master updated (8179779 -> 030bbed)
Charles Plessy
plessy at moszumanska.debian.org
Fri Sep 4 14:29:26 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository bedtools.
from 8179779 Merge https://github.com/arq5x/bedtools2
new d28d1fc 1st check-in: Converted groupby to PFM
new 53ecd3c New unit tests (with bug fixes) for groupby
new b1e3d8d Merge pull request #265 from nkindlon/master
new af0f9fb adds CPPFLAGS to all compilation targets
new 833bd23 Merge branch 'master' into wip-issue-206
new 2d7b550 resolve conflict
new 86bce5c t push origin masterMerge branch 'wookietreiber-wip-issue-206'
new b47dbef settle on uint32_t signature for QuickString. Resolves #267 and #271?
new c730e8e [BUG] fix longstanding bug where genomecov did not report chromosomes with no data at all.
new 5763783 Test compatibility with OS X improved
new 6debe57 OS X compatibility fix
new f678c7f Delete temporary files after test completion
new 462318f Merge pull request #249 from gtamazian/test-fixes
new b588bec Merge branch 'master' of https://github.com/arq5x/bedtools2
new eb03af1 add vcfsort script
new e542de7 add support for -F and -e
new 602d650 missing genomecov test files
new 53f7131 coverage does not need op columns. fixes #287
new e0e4e5d pretty split tests
new e4908d6 missing doc images. fixes #285
new 57929b9 add new tests for -e anf -F options
new e5f7593 update docs for -e and -F
new 4cba483 update history for 2.25.0
new e1062a3 update docs version
new 6ceaef3 Setting Release-Version v2.25.0
new 2bbd748 docs formatting
new 9fb71b2 fix Makefile
new 1d7b0cd Setting Release-Version v2.25.0
new be44824 don't raise a chromosome discrepancy error for unmapped reads in BAM dbs.
new 2f3ef74 tabs to spaces.
new 030bbed Merge branch 'master' of https://github.com/arq5x/bedtools2
The 31 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 | 8 +-
docs/conf.py | 4 +-
docs/content/history.rst | 14 +
docs/content/images/tool-glyphs/random-glyph.ai | 6467 ++++++++++++++++++++
docs/content/images/tool-glyphs/random-glyph.png | Bin 0 -> 30097 bytes
docs/content/tools/coverage.rst | 2 +
docs/content/tools/intersect.rst | 3 +
docs/content/tools/jaccard.rst | 7 +-
docs/content/tools/map.rst | 6 +-
docs/content/tools/subtract.rst | 6 +-
scripts/vcfsort.sh | 13 +
src/annotateBed/Makefile | 2 +-
src/bamToBed/Makefile | 2 +-
src/bamToFastq/Makefile | 2 +-
src/bed12ToBed6/Makefile | 2 +-
src/bedToBam/Makefile | 2 +-
src/bedToIgv/Makefile | 2 +-
src/bedpeToBam/Makefile | 2 +-
src/bedtools.cpp | 6 +-
src/closestFile/Makefile | 2 +-
src/clusterBed/Makefile | 2 +-
src/coverageFile/coverageFile.cpp | 24 +-
src/expand/Makefile | 2 +-
src/fastaFromBed/Makefile | 2 +-
src/fisher/Makefile | 2 +-
src/flankBed/Makefile | 2 +-
src/genomeCoverageBed/Makefile | 2 +-
src/genomeCoverageBed/genomeCoverageBed.cpp | 55 +-
src/genomeCoverageBed/genomeCoverageBed.h | 8 +-
src/getOverlap/Makefile | 2 +-
src/groupBy/Makefile | 38 +-
src/groupBy/groupBy.cpp | 755 +--
src/groupBy/groupBy.h | 41 +
src/groupBy/groupByHelp.cpp | 92 +
src/intersectFile/Makefile | 2 +-
src/jaccard/Makefile | 2 +-
src/linksBed/Makefile | 2 +-
src/mapFile/Makefile | 2 +-
src/maskFastaFromBed/Makefile | 2 +-
src/mergeFile/Makefile | 2 +-
src/multiBamCov/Makefile | 2 +-
src/multiIntersectBed/Makefile | 2 +-
src/nekSandbox1/Makefile | 2 +-
src/nucBed/Makefile | 2 +-
src/pairToBed/Makefile | 2 +-
src/pairToPair/Makefile | 2 +-
src/randomBed/Makefile | 2 +-
src/regressTest/Makefile | 6 +-
src/reldist/Makefile | 2 +-
src/sampleFile/Makefile | 2 +-
src/shuffleBed/Makefile | 2 +-
src/slopBed/Makefile | 2 +-
src/sortBed/Makefile | 2 +-
src/spacingFile/Makefile | 2 +-
src/spacingFile/spacingFile.cpp | 5 +-
src/split/Makefile | 2 +-
src/subtractFile/subtractFile.cpp | 2 +-
src/tagBam/Makefile | 2 +-
src/unionBedGraphs/Makefile | 2 +-
src/utils/BamTools-Ancillary/Makefile | 2 +-
src/utils/BamTools/Makefile | 2 +-
src/utils/BinTree/BinTree.cpp | 12 +-
src/utils/BinTree/Makefile | 2 +-
src/utils/BlockedIntervals/Makefile | 2 +-
src/utils/Contexts/ContextBase.cpp | 30 +-
src/utils/Contexts/ContextBase.h | 17 +-
src/utils/Contexts/ContextClosest.cpp | 11 -
src/utils/Contexts/ContextCoverage.cpp | 7 +-
src/utils/Contexts/ContextCoverage.h | 2 -
src/utils/Contexts/ContextGroupBy.cpp | 138 +
src/utils/Contexts/ContextGroupBy.h | 40 +
src/utils/Contexts/ContextIntersect.cpp | 48 +-
src/utils/Contexts/ContextIntersect.h | 23 +-
src/utils/Contexts/Makefile | 14 +-
src/utils/Fasta/Makefile | 2 +-
.../FileReaders/BufferedStreamMgr.h | 2 +-
src/utils/FileRecordTools/FileReaders/Makefile | 2 +-
src/utils/FileRecordTools/FileReaders/Makefile~ | 2 +-
.../FileReaders/SingleLineDelimTextFileReader.cpp | 7 +-
.../FileReaders/SingleLineDelimTextFileReader.h | 3 +-
src/utils/FileRecordTools/FileRecordMgr.cpp | 26 +-
src/utils/FileRecordTools/FileRecordMgr.h | 6 +-
src/utils/FileRecordTools/Makefile | 4 +-
src/utils/FileRecordTools/Records/Makefile | 7 +-
.../FileRecordTools/Records/NoPosPlusRecord.cpp | 42 +
.../FileRecordTools/Records/NoPosPlusRecord.h | 41 +
src/utils/FileRecordTools/Records/Record.cpp | 61 +-
src/utils/FileRecordTools/Records/Record.h | 14 +-
src/utils/FileRecordTools/Records/RecordMgr.cpp | 21 +
src/utils/FileRecordTools/Records/RecordMgr.h | 1 +
src/utils/FileRecordTools/Records/VcfRecord.cpp | 2 +-
src/utils/GenomeFile/Makefile | 4 +-
src/utils/KeyListOps/Makefile | 2 +-
src/utils/NewChromsweep/Makefile | 2 +-
src/utils/NewChromsweep/NewChromsweep.cpp | 607 +-
src/utils/RecordOutputMgr/Makefile | 2 +-
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 20 +-
src/utils/VectorOps/Makefile | 2 +-
src/utils/bedFile/Makefile | 2 +-
src/utils/bedFilePE/Makefile | 2 +-
src/utils/bedGraphFile/Makefile | 2 +-
src/utils/chromsweep/Makefile | 2 +-
src/utils/{aux => driver}/BedtoolsDriver.cpp | 8 +-
src/utils/{aux => driver}/BedtoolsDriver.h | 0
src/utils/{aux => driver}/Makefile | 0
src/utils/fileType/FileRecordTypeChecker.cpp | 25 +-
src/utils/fileType/FileRecordTypeChecker.h | 5 +-
src/utils/fileType/Makefile | 2 +-
src/utils/general/CommonHelp.cpp | 11 +-
src/utils/general/Makefile | 2 +-
src/utils/general/QuickString.cpp | 39 +-
src/utils/general/QuickString.h | 7 +-
src/utils/gzstream/Makefile | 2 +-
src/utils/sequenceUtilities/Makefile | 2 +-
src/utils/tabFile/Makefile | 2 +-
src/utils/version/Makefile | 2 +-
src/utils/version/version_release.txt | 6 +-
src/windowBed/Makefile | 2 +-
src/windowMaker/Makefile | 2 +-
test/general/test-general.sh | 2 +-
test/genomecov/test-genomecov.sh | 92 +-
test/genomecov/y.bam | Bin 0 -> 220 bytes
test/genomecov/y.bed | 2 +
test/{intersect => groupBy}/a_vcfSVtest.vcf | 0
test/{intersect => groupBy}/gdc.bam | Bin
test/groupBy/noPosvalues.header.bed | 13 +
test/groupBy/test-groupby.sh | 339 +-
test/groupBy/values3.7fields.header.bed | 13 +
.../values3.bed => groupBy/values3.no_header.bed} | 0
.../values3.unmarked_header.bed} | 1 +
test/groupBy/values3_case.header.bed | 13 +
test/intersect/b.bed | 2 +-
test/intersect/e.bed | 1 +
test/intersect/foo | 1 +
.../multi_intersect/test-multi_intersect.sh | 2 +-
test/intersect/{bug223_sv1_b.vcf => svlen.vcf} | 1 +
test/intersect/test-intersect.sh | 136 +-
test/intersect/two_blocks_partial.bam.bai | Bin 0 -> 832 bytes
test/intersect/x.bam | Bin 0 -> 1755 bytes
test/intersect/x.bed | 3 +
test/intersect/y.bed | 2 +
test/sample/test-sample.sh | 1 +
test/split/test-split.sh | 59 +-
143 files changed, 8418 insertions(+), 1258 deletions(-)
create mode 100644 docs/content/images/tool-glyphs/random-glyph.ai
create mode 100644 docs/content/images/tool-glyphs/random-glyph.png
create mode 100755 scripts/vcfsort.sh
create mode 100644 src/groupBy/groupBy.h
create mode 100644 src/groupBy/groupByHelp.cpp
create mode 100644 src/utils/Contexts/ContextGroupBy.cpp
create mode 100644 src/utils/Contexts/ContextGroupBy.h
create mode 100644 src/utils/FileRecordTools/Records/NoPosPlusRecord.cpp
create mode 100644 src/utils/FileRecordTools/Records/NoPosPlusRecord.h
rename src/utils/{aux => driver}/BedtoolsDriver.cpp (94%)
rename src/utils/{aux => driver}/BedtoolsDriver.h (100%)
rename src/utils/{aux => driver}/Makefile (100%)
create mode 100644 test/genomecov/y.bam
create mode 100644 test/genomecov/y.bed
copy test/{intersect => groupBy}/a_vcfSVtest.vcf (100%)
copy test/{intersect => groupBy}/gdc.bam (100%)
create mode 100644 test/groupBy/noPosvalues.header.bed
create mode 100644 test/groupBy/values3.7fields.header.bed
copy test/{map/values3.bed => groupBy/values3.no_header.bed} (100%)
copy test/{map/values3.bed => groupBy/values3.unmarked_header.bed} (91%)
create mode 100644 test/groupBy/values3_case.header.bed
create mode 100644 test/intersect/e.bed
create mode 100644 test/intersect/foo
copy test/intersect/{bug223_sv1_b.vcf => svlen.vcf} (67%)
create mode 100644 test/intersect/two_blocks_partial.bam.bai
create mode 100644 test/intersect/x.bam
create mode 100644 test/intersect/x.bed
create mode 100644 test/intersect/y.bed
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