[med-svn] [bedtools] branch debian/unstable updated (4169a2d -> a374cf4)
Andreas Tille
tille at debian.org
Tue Jul 7 15:10:30 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch debian/unstable
in repository bedtools.
from 4169a2d Further hints
new 9156ebc Fix pritine-tar step description
adds 2d8c5a4 Update README.md
adds 2f4d319 Update conf.py
new 9d4ed4c Fixed bug167: stranded chromsweep wasn't working
new 3ca83fb Merge pull request #168 from nkindlon/master
new 73e435b betools pool
new e53d608 bedtools split
new 1bf6aaf error message
new ea68524 moved from long to double
new a1aa1ae display double/long
new 1ca4359 Merge pull request #170 from lindenb/master
new 3398f72 simple algorithm when n< FOPEN_MAX
new 6e76c8c Merge pull request #172 from lindenb/master
new 2d836be minor cleanup to split
new a6edcc8 added new "spacing" tool to report distances between intervals in a single file.
new 3bea2a7 added note about sorted input.
new 2b1df94 right, the actual spacing code.
new d6547b3 add missing includes
new b561cf5 [BUG] -s is not required with -n
new 068cc3a deprecate -abam and update help to show that -a supports BAM
new 26892d4 formatting
new f9fbaac Merge branch 'master' of https://github.com/nkindlon/bedtools2
new 29fe57f Added closest -fu and -fd, updated help
new 90892a6 Added files
new 24e97cc K closest finally working; chrom name conventions test change
new 60f99fb addressing merge conflict
new 1d1d36d Merge branch 'master' of https://github.com/nkindlon/bedtools2
new 24cdf1f Merge remote-tracking branch 'upstream/master'
new 930ddce Fixing merge errors
new 291f23b src/utils/Contexts/ContextBase.cpp
new 0efb547 Merge error corrections
new 3735ff4 forgot context Makefile
new 217cad4 another merge error
new e7656ff yet another merge error
new ba3bb10 Cahnged Closest's RecDistList class to not use map
new 59b7ab6 Merge pull request #179 from nkindlon/master
new dbc19ad bug fixes for kclosest sorted output, 0 length records, and map a vs b file with multi-dbs
new 4a9a6c2 forgot new test files for intersect unit tests
new 59116f2 Fixed context error that broke merge
new 64b9592 Merge pull request #190 from nkindlon/master
new 33577de Added first and last to help options for -o
new 78c266d Fixed bug for -nonamecheck, added help, unit test
new 6eada05 clean compile, need to test
new 33d4cc2 fix param parsing; add 1 to win number
new d98c7f8 test stub; refactor num_window calculation
new 66b1d64 test stubs; ``-n`` is excepting now
new efda13c all tests pass
new c432a19 Merge pull request #194 from jayhesselberth/reverse-windows
new 8456c20 Setting Release-Version v2.23.0
new 05ecd83 update docs for 2.23.0
new 5cc56ed Merge pull request #201 from nkindlon/master
new 59f252a enable -header for closest.
new e5878aa Merge remote-tracking branch 'upstream/master'
new 4abcc2b Added unit test for closest to check -header option
new 6961cd2 First check-in for new version of subtract
new 706608e added unit tests for -sorted and multiple databases.
new 509e6fe Added -wb and -wo to subtract help
new 488b059 Addressed bug #208; seg fault when VCF doesn't have SVLEN for imprecise variants.
new 567477f Fixed bug 223, Insertions for VCF records. Added unit test.
new 56c6438 Changed -nonamecheck to warning only, added to help for map, closest, jaccard
new 3c14db0 Corrected bug 218 by disabling intra-file name convention checking and allowing -nonamecheck for unsorted files
new 16aa8fb Merge branch 'master' of https://github.com/nkindlon/bedtools2
new 1fcf780 corected unit test files for VCF insertions; changed to min instead of max for SV's with multiple vals
new ed59faa first check in for mass refactor from program to tools API
new 9da6031 forgot src/utils/ToolBase directory
new 5d0f136 Forgot unit test directory for spacing.
new e052d77 first check in for new coverage tool
new d836850 Fixed bug where name conventions weren't tested for unsorted data; stopped namecheck on unmapped bam records
new 5b4e0f7 Merge branch 'master' of https://www.github.com/nkindlon/bedtools2
new 43006c9 Fixed BedPlus bug, now only requires first 3 fields instead of 6
new 9f2d849 Unit tests for coverge, corrections to -split behavior for jaccard and fisher, minor code clean up
new 0fd6eab Changed help in all tools to use common help
new 3dc3075 forgot a.bed in unit tests for coverage
new ad9efaa forgot b.bed in coverage unit tests
new 702f78e Fixed sample unit test
new 5b00dce revcomp support for IUPAC
new 237766a add tests for getfasta
new e2add0f Merge pull request #202 from nkindlon/master
new 5cc7706 Merge pull request #203 from nkindlon/master
new 447cb97 Update README.md
new 81f458f Merge pull request #204 from nkindlon/master
new e65c98b Merge branch 'master' of https://github.com/arq5x/bedtools2
new ada04b6 fix merge docs on how to report strand with . Thanks to @balwierz.
new 83c6faa sort BED on faidx file
new 43f88db Merge pull request #219 from lindenb/sortOnRef
new cbad1fc cleanup
new 7553f4a Merge pull request #222 from nkindlon/master
new 47bdc32 Merge pull request #224 from nkindlon/master
new 979cf77 Fix a crash bug (when end == -1).
new ab600e6 Merge pull request #231 from yanlinlin82/master
new 84a4f05 Merge pull request #225 from nkindlon/master
new ed38d47 merge cleanup
new 6639785 fix help to reflect interface change
new 3658be1 Move "using namespace std" after #includes
new 5015702 Avoid overflow in int2str()
new 7b28060 Minor makefile improvments
new b37d274 merge conflicts
new df1de0d Merge branch 'jmarshall-warnings3'
new 54f37af merge conflict
new 0d0dff8 Fixed some merge errors
new 60022b9 Fixed build break in CommonHelp
new 5827f9c Merge pull request #239 from nkindlon/master
new cc963ef Tests for IUPAC processing fixed
new 0b73675 Show warning if a FASTA index file is outdated
new e2b4e53 Merge pull request #242 from gtamazian/getfasta-fixes
new 3010bf5 Addressed BinTree memory blow-up; -m in fisher (w/ unit tests)
new e4955d3 Merge pull request #243 from nkindlon/master
new 0fa2515 only set end to 1 if slop is negative and rolls off start of chrom
new c621014 tweak test
new a0778bf update coverage docs
new 070ff0d update the help for coverage to reflect new role of A versus B.
new 76aa9d7 add note about CLI change for coverage
new 8edf266 Removed accidental copy in BinTree to fix speed
new 5f0362f Changed common help to remove -names, -filenames, and -sortout from all tools but intersect and closest.
new 33f2bef Merge pull request #244 from nkindlon/master
new ca31d1f Addressed >2 numbers in VCF SVLEN, can appear at endl w/ tab, semi-colon, newline or null
new 9724fbb Added extra unit test for vcf svlen - single # at end of line
new 9b8e84b Merge pull request #245 from nkindlon/master
new 0def600 update release history for 2.24.0
new b0c34da bump docs version
new d6535fc Setting Release-Version v2.24.0
new fc8ae41 Merge tag 'v2.24.0' into debian/unstable
new a374cf4 Refresh patches
The 121 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 | 51 +-
README.md | 2 +-
debian/README.source | 4 +-
debian/changelog | 7 +-
debian/patches/gzstream.h.patch | 2 -
docs/conf.py | 12 +-
docs/content/history.rst | 47 ++
docs/content/tools/closest.rst | 8 +
docs/content/tools/coverage.rst | 207 +++---
docs/content/tools/merge.rst | 14 +-
src/bedtools.cpp | 152 +++--
src/closestFile/Makefile | 12 +-
src/closestFile/closestFile.cpp | 80 +--
src/closestFile/closestFile.h | 63 +-
.../{closestMain.cpp => closestHelp.cpp} | 199 +++---
src/coverageBed/Makefile | 35 -
src/coverageBed/coverageBed.cpp | 341 ----------
src/coverageBed/coverageBed.h | 83 ---
src/coverageBed/coverageMain.cpp | 180 ------
src/{jaccard => coverageFile}/Makefile | 18 +-
src/coverageFile/coverageFile.cpp | 203 ++++++
src/coverageFile/coverageFile.h | 54 ++
src/coverageFile/coverageHelp.cpp | 50 ++
src/fisher/Fisher.h | 39 --
src/fisher/Makefile | 40 +-
src/fisher/{Fisher.cpp => fisher.cpp} | 102 ++-
src/fisher/fisher.h | 37 ++
src/fisher/fisherHelp.cpp | 29 +
src/fisher/fisherMain.cpp | 71 ---
src/fisher/{kfunc.c => kfunc.cpp} | 22 +-
src/fisher/kfunc.h | 40 ++
src/genomeCoverageBed/genomeCoverageBed.cpp | 2 +-
src/intersectFile/Makefile | 7 +-
src/intersectFile/intersectFile.cpp | 137 ++--
src/intersectFile/intersectFile.h | 44 +-
src/intersectFile/intersectHelp.cpp | 47 ++
src/intersectFile/intersectMain.cpp | 146 -----
src/jaccard/Jaccard.cpp | 94 ---
src/jaccard/Jaccard.h | 39 --
src/jaccard/Makefile | 11 +-
src/jaccard/jaccard.cpp | 79 +++
src/jaccard/jaccard.h | 41 ++
src/jaccard/jaccardHelp.cpp | 40 ++
src/jaccard/jaccardMain.cpp | 191 ------
src/mapFile/Makefile | 25 +-
src/mapFile/mapFile.cpp | 64 +-
src/mapFile/mapFile.h | 52 +-
src/mapFile/mapHelp.cpp | 36 ++
src/mapFile/mapMain.cpp | 91 ---
src/mergeFile/Makefile | 10 +-
src/mergeFile/mergeFile.cpp | 61 +-
src/mergeFile/mergeFile.h | 57 +-
src/mergeFile/{mergeMain.cpp => mergeHelp.cpp} | 42 +-
src/nekSandbox1/nekSandboxMain.cpp | 22 +-
src/sampleFile/Makefile | 9 +-
src/sampleFile/SampleFile.h | 43 --
src/sampleFile/{SampleFile.cpp => sampleFile.cpp} | 61 +-
src/sampleFile/sampleFile.h | 47 ++
src/sampleFile/{sampleMain.cpp => sampleHelp.cpp} | 37 +-
src/slopBed/slopBed.cpp | 8 +-
src/sortBed/sortBed.cpp | 69 +-
src/sortBed/sortBed.h | 7 +-
src/sortBed/sortMain.cpp | 30 +-
src/{sampleFile => spacingFile}/Makefile | 11 +-
src/spacingFile/spacingFile.cpp | 82 +++
src/spacingFile/spacingFile.h | 43 ++
src/spacingFile/spacingHelp.cpp | 43 ++
src/{subtractBed => split}/Makefile | 7 +-
src/split/splitBed.cpp | 359 +++++++++++
src/{randomBed/randomBed.h => split/splitBed.h} | 55 +-
src/split/splitBedMain.cpp | 20 +
src/subtractBed/subtractBed.cpp | 191 ------
src/subtractBed/subtractBed.h | 57 --
src/subtractBed/subtractMain.cpp | 173 -----
src/{intersectFile => subtractFile}/Makefile | 13 +-
src/subtractFile/subtractFile.cpp | 134 ++++
src/subtractFile/subtractFile.h | 36 ++
src/subtractFile/subtractHelp.cpp | 43 ++
src/utils/BinTree/BinTree.cpp | 136 +---
src/utils/BinTree/BinTree.h | 40 +-
src/utils/Contexts/ContextBase.cpp | 136 +++-
src/utils/Contexts/ContextBase.h | 32 +-
src/utils/Contexts/ContextClosest.cpp | 63 +-
src/utils/Contexts/ContextClosest.h | 10 +-
src/utils/Contexts/ContextCoverage.cpp | 78 +++
src/utils/Contexts/ContextCoverage.h | 40 ++
src/utils/Contexts/ContextFisher.cpp | 98 +--
src/utils/Contexts/ContextFisher.h | 11 +-
src/utils/Contexts/ContextIntersect.cpp | 12 -
src/utils/Contexts/ContextIntersect.h | 5 +-
src/utils/Contexts/ContextJaccard.cpp | 18 -
src/utils/Contexts/ContextJaccard.h | 2 +-
src/utils/Contexts/ContextMap.cpp | 11 -
src/utils/Contexts/ContextMerge.cpp | 8 -
src/utils/Contexts/ContextSample.cpp | 12 -
src/utils/Contexts/ContextSpacing.cpp | 29 +
src/utils/Contexts/ContextSpacing.h | 25 +
src/utils/Contexts/ContextSubtract.cpp | 89 +++
src/utils/Contexts/ContextSubtract.h | 37 ++
src/utils/Contexts/Makefile | 11 +-
src/utils/Fasta/Fasta.cpp | 9 +-
.../FileReaders/SingleLineDelimTextFileReader.cpp | 48 +-
src/utils/FileRecordTools/Makefile | 9 +-
src/utils/FileRecordTools/Records/BamRecord.cpp | 20 +
src/utils/FileRecordTools/Records/BamRecord.h | 3 +
.../FileRecordTools/Records/Bed12Interval.cpp | 20 +
src/utils/FileRecordTools/Records/Bed12Interval.h | 1 +
.../FileRecordTools/Records/BedPlusInterval.cpp | 47 +-
.../FileRecordTools/Records/BedPlusInterval.h | 14 +-
src/utils/FileRecordTools/Records/BlockMgr.cpp | 10 +-
src/utils/FileRecordTools/Records/BlockMgr.h | 7 +-
src/utils/FileRecordTools/Records/Record.cpp | 19 +-
src/utils/FileRecordTools/Records/Record.h | 3 +-
.../FileRecordTools/Records/RecordKeyVector.cpp | 55 +-
.../FileRecordTools/Records/RecordKeyVector.h | 8 +-
src/utils/FileRecordTools/Records/VcfRecord.cpp | 14 +-
src/utils/FileRecordTools/Records/VcfRecord.h | 7 +-
src/utils/KeyListOps/KeyListOps.cpp | 7 +
src/utils/NewChromsweep/CloseSweep.cpp | 702 ++++++++++++++-------
src/utils/NewChromsweep/CloseSweep.h | 98 ++-
src/utils/NewChromsweep/NewChromsweep.cpp | 9 +-
src/utils/NewChromsweep/NewChromsweep.h | 6 +-
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 41 +-
src/utils/RecordOutputMgr/RecordOutputMgr.h | 13 +-
src/utils/{RecordOutputMgr => ToolBase}/Makefile | 79 +--
src/utils/ToolBase/ToolBase.cpp | 4 +
src/utils/ToolBase/ToolBase.h | 35 +
src/utils/aux/BedtoolsDriver.cpp | 144 +++++
src/utils/aux/BedtoolsDriver.h | 16 +
src/utils/aux/Makefile | 93 +++
src/utils/bedFile/bedFile.h | 36 +-
src/utils/fileType/FileRecordTypeChecker.cpp | 27 +-
src/utils/fileType/FileRecordTypeChecker.h | 7 +-
src/utils/general/CommonHelp.cpp | 96 ++-
src/utils/general/CommonHelp.h | 12 +-
src/utils/general/ErrorMsg.cpp | 2 +
src/utils/general/ErrorMsg.h | 1 -
src/utils/general/Makefile | 5 +-
src/utils/general/ParseTools.cpp | 2 +-
src/utils/general/ParseTools.h | 44 +-
src/utils/general/QuickString.cpp | 14 +
src/utils/general/QuickString.h | 3 +
src/utils/sequenceUtilities/sequenceUtils.cpp | 89 +++
src/utils/version/version_release.txt | 6 +-
src/windowMaker/windowMaker.cpp | 37 +-
src/windowMaker/windowMaker.h | 8 +-
src/windowMaker/windowMakerMain.cpp | 35 +-
test/closest/a.bed | 1 +
test/closest/{bug157_a.bed => a2.bed} | 0
test/closest/{bug157_b.bed => b2.bed} | 0
test/closest/d4.bed | 2 +
test/closest/kclosest/d1.bed | 7 +
test/closest/kclosest/d2.bed | 9 +
test/closest/kclosest/d3.bed | 18 +
test/closest/kclosest/q1.bed | 1 +
test/closest/kclosest/q2.bed | 2 +
test/closest/kclosest/test-kclosest.sh | 654 +++++++++++++++++++
test/closest/sortAndNaming/test-sort-and-naming.sh | 8 +-
test/closest/test-closest.sh | 16 +
test/coverage/a.bed | 6 +
test/coverage/b.bed | 20 +
test/coverage/test-coverage.sh | 442 ++++++++++++-
test/fisher/{a.bed => a_merge.bed} | 1 +
test/fisher/test-fisher.sh | 42 ++
test/general/test-general.sh | 8 +-
test/getfasta/test-getfasta.sh | 45 +-
test/getfasta/test.iupac.bed | 2 +
test/getfasta/test.iupac.fa | 4 +
test/intersect/bug167_strandSweep.bed | 10 +
test/intersect/bug187_a.bed | 1 +
test/intersect/bug187_b.bed | 2 +
test/intersect/bug223_e.vcf | 3 +
test/intersect/bug223_f.vcf | 3 +
test/intersect/bug223_sv1_a.vcf | 3 +
test/intersect/bug223_sv1_b.vcf | 3 +
test/intersect/new_test-intersect.sh | 6 +-
.../{closest/a.bed => intersect/nonamecheck_a.bed} | 0
test/intersect/nonamecheck_b.bed | 1 +
.../sortAndNaming/test-sort-and-naming.sh | 8 +-
test/intersect/test-intersect.sh | 119 ++++
test/jaccard/a.bed | 1 +
test/jaccard/test-jaccard.sh | 7 +-
test/makewindows/input.bed | 4 +
test/makewindows/test-makewindows.sh | 128 ++++
test/merge/test-merge.sh | 2 +-
test/sample/sample_help_withoutVersion.txt | 33 -
test/sample/test-sample.sh | 6 +-
test/spacing/a.bed | 8 +
test/spacing/test-spacing.sh | 28 +
test/split/test-split.sh | 25 +
test/subtract/b2.bed | 2 +
test/subtract/d.bed | 1 +
test/subtract/test-subtract.sh | 144 ++++-
test/test.sh | 5 +
194 files changed, 6317 insertions(+), 3512 deletions(-)
rename src/closestFile/{closestMain.cpp => closestHelp.cpp} (64%)
delete mode 100644 src/coverageBed/Makefile
delete mode 100644 src/coverageBed/coverageBed.cpp
delete mode 100644 src/coverageBed/coverageBed.h
delete mode 100644 src/coverageBed/coverageMain.cpp
copy src/{jaccard => coverageFile}/Makefile (80%)
create mode 100644 src/coverageFile/coverageFile.cpp
create mode 100644 src/coverageFile/coverageFile.h
create mode 100644 src/coverageFile/coverageHelp.cpp
delete mode 100644 src/fisher/Fisher.h
rename src/fisher/{Fisher.cpp => fisher.cpp} (60%)
create mode 100644 src/fisher/fisher.h
create mode 100644 src/fisher/fisherHelp.cpp
delete mode 100644 src/fisher/fisherMain.cpp
rename src/fisher/{kfunc.c => kfunc.cpp} (93%)
create mode 100644 src/fisher/kfunc.h
create mode 100644 src/intersectFile/intersectHelp.cpp
delete mode 100644 src/intersectFile/intersectMain.cpp
delete mode 100644 src/jaccard/Jaccard.cpp
delete mode 100644 src/jaccard/Jaccard.h
create mode 100644 src/jaccard/jaccard.cpp
create mode 100644 src/jaccard/jaccard.h
create mode 100644 src/jaccard/jaccardHelp.cpp
delete mode 100644 src/jaccard/jaccardMain.cpp
create mode 100644 src/mapFile/mapHelp.cpp
delete mode 100644 src/mapFile/mapMain.cpp
rename src/mergeFile/{mergeMain.cpp => mergeHelp.cpp} (60%)
delete mode 100644 src/sampleFile/SampleFile.h
rename src/sampleFile/{SampleFile.cpp => sampleFile.cpp} (72%)
create mode 100644 src/sampleFile/sampleFile.h
rename src/sampleFile/{sampleMain.cpp => sampleHelp.cpp} (63%)
copy src/{sampleFile => spacingFile}/Makefile (82%)
create mode 100644 src/spacingFile/spacingFile.cpp
create mode 100644 src/spacingFile/spacingFile.h
create mode 100644 src/spacingFile/spacingHelp.cpp
rename src/{subtractBed => split}/Makefile (82%)
create mode 100644 src/split/splitBed.cpp
copy src/{randomBed/randomBed.h => split/splitBed.h} (50%)
create mode 100644 src/split/splitBedMain.cpp
delete mode 100644 src/subtractBed/subtractBed.cpp
delete mode 100644 src/subtractBed/subtractBed.h
delete mode 100644 src/subtractBed/subtractMain.cpp
copy src/{intersectFile => subtractFile}/Makefile (79%)
create mode 100644 src/subtractFile/subtractFile.cpp
create mode 100644 src/subtractFile/subtractFile.h
create mode 100644 src/subtractFile/subtractHelp.cpp
create mode 100644 src/utils/Contexts/ContextCoverage.cpp
create mode 100644 src/utils/Contexts/ContextCoverage.h
create mode 100644 src/utils/Contexts/ContextSpacing.cpp
create mode 100644 src/utils/Contexts/ContextSpacing.h
create mode 100644 src/utils/Contexts/ContextSubtract.cpp
create mode 100644 src/utils/Contexts/ContextSubtract.h
copy src/utils/{RecordOutputMgr => ToolBase}/Makefile (86%)
create mode 100644 src/utils/ToolBase/ToolBase.cpp
create mode 100644 src/utils/ToolBase/ToolBase.h
create mode 100644 src/utils/aux/BedtoolsDriver.cpp
create mode 100644 src/utils/aux/BedtoolsDriver.h
create mode 100644 src/utils/aux/Makefile
create mode 100644 src/utils/general/ErrorMsg.cpp
copy test/closest/{bug157_a.bed => a2.bed} (100%)
copy test/closest/{bug157_b.bed => b2.bed} (100%)
create mode 100644 test/closest/d4.bed
create mode 100644 test/closest/kclosest/d1.bed
create mode 100644 test/closest/kclosest/d2.bed
create mode 100644 test/closest/kclosest/d3.bed
create mode 100644 test/closest/kclosest/q1.bed
create mode 100644 test/closest/kclosest/q2.bed
create mode 100644 test/closest/kclosest/test-kclosest.sh
create mode 100644 test/coverage/a.bed
create mode 100644 test/coverage/b.bed
copy test/fisher/{a.bed => a_merge.bed} (75%)
create mode 100644 test/getfasta/test.iupac.bed
create mode 100644 test/getfasta/test.iupac.fa
create mode 100644 test/intersect/bug167_strandSweep.bed
create mode 100644 test/intersect/bug187_a.bed
create mode 100644 test/intersect/bug187_b.bed
create mode 100644 test/intersect/bug223_e.vcf
create mode 100644 test/intersect/bug223_f.vcf
create mode 100644 test/intersect/bug223_sv1_a.vcf
create mode 100644 test/intersect/bug223_sv1_b.vcf
copy test/{closest/a.bed => intersect/nonamecheck_a.bed} (100%)
create mode 100644 test/intersect/nonamecheck_b.bed
create mode 100644 test/makewindows/input.bed
create mode 100644 test/makewindows/test-makewindows.sh
delete mode 100644 test/sample/sample_help_withoutVersion.txt
create mode 100644 test/spacing/a.bed
create mode 100644 test/spacing/test-spacing.sh
create mode 100644 test/split/test-split.sh
create mode 100644 test/subtract/b2.bed
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