[med-svn] [bedtools] branch master updated (8179779 -> 030bbed)

Charles Plessy plessy at moszumanska.debian.org
Fri Sep 4 14:29:26 UTC 2015


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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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