[med-svn] [bedtools] branch debian/unstable updated (6835466 -> b757049)
Charles Plessy
plessy at moszumanska.debian.org
Mon Jan 5 01:05:05 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch debian/unstable
in repository bedtools.
from 6835466 bedtools (2.21.0-1) unstable; urgency=medium
adds 51ef360 fix #117 by re-ordering contingency table. thanks @thomasgilgenast for a clear report
adds c7c9078 Merge pull request #126 from brentp/contingency-order
adds 479a2fc [ENH] add -prec to control decimal point precision in groupby
adds 15b2539 step must be non-zero
adds 4c0dd78 add Netbeans folder “nbproject” to .gitignore
adds 21f53b7 fix comment typo
adds 41f96cf fix bamToFastq skipping reads after unpaired reads
adds 62802ec Merge pull request #132 from ryan-williams/fastq
adds f1d7c76 better precision in reporting for fisher
adds a5bd6db tabs -> spaces
adds e6f1418 Merge pull request #134 from brentp/fisher-precision
adds 81d2ada Merge branch 'master' of https://github.com/arq5x/bedtools2
adds 1b707ee update stable release information.
adds 13e4308 track _templates for docs
adds 5b47f91 cleanup
adds 54e27a1 First check-in for new closest tool
adds 8cc9c0a Adding corrected Makefile
adds 34f0dd7 Forgot RecordOutputMgr
adds 897d1a8 first check-in for new closest tool
adds 8a2e369 Bug fixes and more unit tests for closest
adds 5d20ecf Corrections and unit tests for closest -D option.
adds 267cb42 Fixed one more bug with tie mode resolution when using mdb's.
adds 7b2a560 Including files for minor fixes omitted in yesterday's check-in
adds 31878f3 merge conflicts
adds 5ba347e Fixed bug 100, allowing scientific notation for coords, not returning INT_MIN for invalid numbers
adds 0ea1769 Fixed bug133, missing intersection of zero length records
adds 0b8612d Read VCF struct vars length from SVLEN tag instead of using length of varRef field
adds 858cc4b VcfRecord code cleanup, add intersect unit test test for VCF SV's.
adds 2f90e6a Merge pull request #139 from nkindlon/master
adds 85f5a10 Setting Release-Version v2.22.0
adds e0fdbbf doc tweaks
adds 91928cf update docs version
adds a60ae74 restore defaukt precision in groupby
adds e7379ae adds make install target
adds 0292f31 Merge pull request #142 from wookietreiber/wip-make-install-target
adds 5f91a5b changed compare function to have "unsigned int"
adds 5926946 Merge pull request #143 from arjanvandervelde/patch-1
adds 296866f Merge branch 'master' of https://github.com/arq5x/bedtools2
adds 418e5d9 add tutorial to docs
adds a52fee4 added tutorial
adds f542c99 restore TOC
adds 39cec40 better tutorial
adds 3b5afaf added -prec option, default 10. Updated unit tests for merge, map, jaccard. Accept stdin by default in merge.
adds 4c6a312 Merge pull request #146 from nkindlon/master
adds 2480322 Merge branch 'master' of https://github.com/arq5x/bedtools2
adds 89805de fix formatting of fisher table
adds fc7d185 Merge pull request #149 from daler/master
adds e1f71df initial go at -exclude for fisher
adds a277bba reorganize contingency table
adds d6544e0 change fisher to use numbers of intervals rather than bases of overlap
adds c3ab3d1 scripts for comparing to shuffled
adds 3594e98 prevent < 0 in n21
adds 548bcae add -m option to merge intervals
adds ed4e8a9 tuning, testing and docs for fisher
adds cf911bf merge conflicts. integrate @brentp's nice improvments to fisher.
adds 205db6a Merge branch 'brentp-fisher-include'
adds 6ae9016 update NewChromSweep signature to support fisher. May have conflicts with @nkindlon's upcoming changes. Will resolve then.
adds 0f4652d [BUG] Fix for issue #153. makewindows -s should not be required with -b.
adds dabde35 Issue 123. Correct genomecov glyph. Thanks to @tdhock for the catch.
adds e63d83e Fix for issue #145. -f was incorrectly set to 0.0 when using -labels, -intervals, or -names.
adds b7ceea4 [BUG] fix for issue #140. chromosome boundaries not properly handled when slop values are negative. Thanks to @acdaugherty for the catch.
adds 92b9249 fixes to tutorial
adds 90af6a7 allow closest ties that don't overlap.
adds 1db6b68 Corrected error in reporting amount of overlap (issue #150)
adds 49a3598 Fix for issue #155
adds d8e5ba5 Merge pull request #151 from tleonardi/master
adds 4c7213c Detect differently ordered files in chromsweep and closest. Merged Fisher changes.
adds 758cd6a Correcting merge conflicts in NewChromsweep.h and .cpp
adds b561a2f Updated jaccard unit test to reflect chromsweep change
adds a2cacdf Cleaned up error message for sort order detection of missing chrom
adds d819c40 Fix for bug 150, closest hangs with -d and tie first mode
adds b70b6ca Added tleonardi's changes for bug 150 re: overlap bases with -split in intersect
adds 436e6f4 Bug fixes for closest and bug 155
adds 50ae752 changes for request #125: return non-zero on errors.
adds cf21ba5 Merge branch 'master' of https://github.com/nkindlon/bedtools2
adds 2a2ae0c Forgot a new test file for closest
adds 4422985 More sort order unit tests for chromsweep and closest; bug fixes and minor enhancements
adds e94c559 Removed large closest tests from repository
adds 2661889 Removed test debugging files from repository
adds 7fd03d3 Merge pull request #152 from nkindlon/master
adds effc83e Fixed bug157: ties not prevented by -iu/-id
adds b3bcab1 Merge pull request #163 from nkindlon/master
adds d736f16 fix conflict
adds ab663c4 updates to closest's docs
adds e194c15 typo
adds 823a1fc change order
adds 9fdb22f bigger font
adds df4e52b goof in mdb -k 2 example.
adds 042294d updates to closest docs
adds 4983727 Fixed bug164, closest runs slower with -id
adds 6744fd0 Merge pull request #165 from nkindlon/master
adds a6e1ecb Merge branch 'master' of https://github.com/arq5x/bedtools2
adds 330bfb5 [DOC] update docs for closest and intersect.
adds 4119372 update help messages.
adds 60111a3 fix tutorial makefile
adds a596d5a Setting Release-Version v2.22.1
new b757049 Merge tag 'v2.22.1' into debian/unstable
The 1 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:
.gitignore | 5 +
Makefile | 10 +-
README.md | 2 +-
docs/conf.py | 4 +-
docs/content/images/fisher/res-genes.png | Bin 0 -> 72950 bytes
docs/content/images/tool-glyphs/closest-glyph.png | Bin 0 -> 138680 bytes
.../content/images/tool-glyphs/genomecov-glyph.png | Bin 41644 -> 43832 bytes
docs/content/tools/closest.rst | 457 +-
docs/content/tools/fisher.rst | 94 +-
docs/content/tools/intersect.rst | 369 +-
docs/index.rst | 11 +-
src/bamToFastq/bamToFastq.cpp | 14 +-
src/bedtools.cpp | 12 +-
src/closestBed/Makefile | 32 -
src/closestBed/closestBed.cpp | 289 -
src/closestBed/closestBed.h | 66 -
src/closestBed/closestMain.cpp | 245 -
src/{mergeFile => closestFile}/Makefile | 90 +-
src/closestFile/closestFile.cpp | 45 +
src/closestFile/closestFile.h | 31 +
src/closestFile/closestMain.cpp | 112 +
src/fisher/Fisher.cpp | 171 +-
src/fisher/Fisher.h | 9 +
src/fisher/Makefile | 35 +-
src/fisher/fisherMain.cpp | 11 +-
src/groupBy/groupBy.cpp | 55 +-
src/intersectFile/intersectFile.cpp | 3 +
src/intersectFile/intersectMain.cpp | 6 +-
src/jaccard/jaccardMain.cpp | 2 +-
src/mapFile/mapMain.cpp | 2 +-
src/mergeFile/mergeMain.cpp | 2 +-
src/pairToPair/pairToPair.cpp | 4 +-
src/sampleFile/sampleMain.cpp | 2 +-
src/slopBed/slopBed.cpp | 12 +-
src/tagBam/tagBam.cpp | 6 +-
src/tagBam/tagBamMain.cpp | 4 +
src/utils/BinTree/BinTree.cpp | 2 +
src/utils/Contexts/ContextBase.cpp | 119 +-
src/utils/Contexts/ContextBase.h | 23 +-
src/utils/Contexts/ContextClosest.cpp | 222 +
src/utils/Contexts/ContextClosest.h | 65 +
src/utils/Contexts/ContextFisher.cpp | 25 +-
src/utils/Contexts/ContextFisher.h | 7 +
src/utils/Contexts/ContextIntersect.cpp | 5 +
src/utils/Contexts/ContextMerge.cpp | 14 +-
src/utils/Contexts/Makefile | 10 +-
.../FileReaders/SingleLineDelimTextFileReader.cpp | 17 +
.../FileReaders/SingleLineDelimTextFileReader.h | 12 +
src/utils/FileRecordTools/Records/BlockMgr.cpp | 7 +-
src/utils/FileRecordTools/Records/Record.cpp | 46 +-
src/utils/FileRecordTools/Records/Record.h | 4 +
src/utils/FileRecordTools/Records/VcfRecord.cpp | 24 +-
src/utils/FileRecordTools/Records/VcfRecord.h | 2 +-
src/utils/KeyListOps/KeyListOps.cpp | 29 +-
src/utils/KeyListOps/KeyListOps.h | 6 +
src/utils/NewChromsweep/CloseSweep.cpp | 525 +
src/utils/NewChromsweep/CloseSweep.h | 57 +
src/utils/NewChromsweep/Makefile | 80 +-
src/utils/NewChromsweep/NewChromsweep.cpp | 707 +-
src/utils/NewChromsweep/NewChromsweep.h | 62 +-
src/utils/RecordOutputMgr/Makefile | 78 +-
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 978 +-
src/utils/RecordOutputMgr/RecordOutputMgr.h | 148 +-
src/utils/bedFile/bedFile.cpp | 18 +-
src/utils/bedFile/bedFile.h | 1 +
src/utils/general/ParseTools.cpp | 29 +-
src/utils/general/ParseTools.h | 8 +-
src/utils/version/version_release.txt | 6 +-
src/windowMaker/windowMakerMain.cpp | 4 +
test/bamtofastq/golden.fq | 8 +
test/bamtofastq/golden.fq2 | 8 +
test/bamtofastq/test-bamtofastq.sh | 20 +
test/bamtofastq/test.sam | 7 +
test/closest/bug157_a.bed | 1 +
test/closest/bug157_b.bed | 2 +
test/closest/close-b.bed | 3 -
test/closest/d.bed | 1 +
test/closest/d_d1F.bed | 1 +
test/closest/d_d1R.bed | 1 +
test/closest/d_d2F.bed | 1 +
test/closest/d_d2R.bed | 1 +
test/closest/d_id.bed | 2 +
test/closest/d_iu.bed | 2 +
test/closest/d_q1.bed | 1 +
test/closest/d_q2.bed | 1 +
test/closest/mdb1.bed | 4 +
test/closest/mdb2.bed | 3 +
test/closest/mdb3.bed | 2 +
test/closest/mq1.bed | 1 +
.../sortAndNaming/alpha_all.bed} | 6 +-
test/closest/sortAndNaming/alpha_missing.bed | 3 +
test/closest/sortAndNaming/db1_gls.bed | 12 +
test/closest/sortAndNaming/db1_leadingZero.txt | 10 +
test/closest/sortAndNaming/db1_noChr.bed | 10 +
test/closest/sortAndNaming/db1_num.bed | 6 +
test/closest/sortAndNaming/db2_num.bed | 6 +
test/closest/sortAndNaming/db2_numBackwards.bed | 6 +
test/closest/sortAndNaming/db3_numBackwards.bed | 4 +
.../sortAndNaming/num_all.bed} | 4 +-
test/closest/sortAndNaming/num_missing.bed | 3 +
test/closest/sortAndNaming/q1_gls.bed | 12 +
test/closest/sortAndNaming/q1_num.bed | 10 +
test/closest/sortAndNaming/q1a_num.bed | 11 +
test/closest/sortAndNaming/sdb1.bed | 2 +
test/closest/sortAndNaming/sq1.bed | 2 +
test/closest/sortAndNaming/test-sort-and-naming.sh | 320 +
test/closest/strand-test-c.bed | 2 +
test/closest/strand-test-d.bed | 2 +
test/closest/test-closest.sh | 519 +-
test/fisher/README.md | 20 +
test/fisher/a.bed | 3 +
test/fisher/b.bed | 2 +
test/fisher/cmp.sh | 9 +
test/fisher/plot.py | 46 +
test/fisher/shuf.sh | 14 +
test/fisher/sim.py | 31 +
test/fisher/t.500.genome | 1 +
test/fisher/t.60.genome | 1 +
test/fisher/test-fisher.sh | 53 +
test/groupBy/test-groupby.sh | 29 +
test/intersect/a_testZeroLen.bed | 3 +
test/intersect/a_vcfSVtest.vcf | 5 +
test/intersect/b_testZeroLen.bed | 2 +
test/intersect/b_vcfSVtest.vcf | 5 +
test/intersect/bug150_a.bed | 1 +
test/intersect/bug150_b.bed | 2 +
test/intersect/new_test-intersect.sh | 59 +-
.../sortAndNaming/alpha_all.bed} | 6 +-
test/intersect/sortAndNaming/alpha_missing.bed | 3 +
.../sortAndNaming/bigTests/2.21_500Kvs500K.txt | 15821 +
test/intersect/sortAndNaming/bigTests/2.21_5v5.txt | 15821 +
.../intersect/sortAndNaming/bigTests/2.21_chr1.txt | 1173 +
.../sortAndNaming/bigTests/curr500Kvs500K.txt | 15575 +
test/intersect/sortAndNaming/bigTests/curr5v5.txt | 15821 +
test/intersect/sortAndNaming/bigTests/currChr1.txt | 1173 +
test/intersect/sortAndNaming/bigTests/db500K.bed | 500000 ++++++++++++++++++
test/intersect/sortAndNaming/bigTests/dbchr1.bed | 39409 ++
test/intersect/sortAndNaming/bigTests/diffs.txt | 34 +
test/intersect/sortAndNaming/bigTests/q500K.bed | 500000 ++++++++++++++++++
test/intersect/sortAndNaming/bigTests/qchr1.bed | 39544 ++
test/intersect/sortAndNaming/db1_gls.bed | 12 +
test/intersect/sortAndNaming/db1_leadingZero.txt | 10 +
test/intersect/sortAndNaming/db1_noChr.bed | 10 +
test/intersect/sortAndNaming/db1_num.bed | 6 +
test/intersect/sortAndNaming/db2_num.bed | 6 +
test/intersect/sortAndNaming/db2_numBackwards.bed | 6 +
test/intersect/sortAndNaming/db3_numBackwards.bed | 4 +
test/intersect/sortAndNaming/diffs.txt | 489 +
test/intersect/sortAndNaming/exp1 | 2 +
.../sortAndNaming/num_all.bed} | 4 +-
test/intersect/sortAndNaming/num_missing.bed | 3 +
test/intersect/sortAndNaming/q1_gls.bed | 12 +
test/intersect/sortAndNaming/q1_num.bed | 10 +
test/intersect/sortAndNaming/q1a_num.bed | 11 +
test/intersect/sortAndNaming/sdb1.bed | 2 +
test/intersect/sortAndNaming/sq1.bed | 2 +
.../sortAndNaming/test-sort-and-naming.sh | 315 +
test/intersect/splitBug155_a.bed | 1 +
test/intersect/splitBug155_b.bed | 1 +
test/intersect/test-intersect.sh | 52 +-
test/jaccard/d.bed | 1 -
test/jaccard/test-jaccard.sh | 11 +-
test/map/test-map.sh | 10 +-
test/merge/bamCol4Mean.txt | 14 +-
test/merge/bamCol5Mean.txt | 14 +-
test/merge/bamCol8Mean.txt | 32 +-
test/merge/bamCol9Mean.txt | 18 +-
test/merge/expFormat.bed | 1 +
test/merge/precisionTest2.bed | 5 +
test/merge/test-merge.sh | 64 +
test/merge/vcfSVtest.vcf | 5 +
test/test.sh | 3 +
tutorial/Makefile | 3 +
tutorial/answers.html | 148 +
tutorial/answers.md | 140 +
tutorial/bedtools.html | 582 +
tutorial/bedtools.md | 716 +
tutorial/bootstrap.css | 4480 +
tutorial/template.class.html | 65 +
tutorial/template.html | 75 +
180 files changed, 1156459 insertions(+), 2124 deletions(-)
create mode 100644 docs/content/images/fisher/res-genes.png
create mode 100644 docs/content/images/tool-glyphs/closest-glyph.png
delete mode 100644 src/closestBed/Makefile
delete mode 100644 src/closestBed/closestBed.cpp
delete mode 100644 src/closestBed/closestBed.h
delete mode 100644 src/closestBed/closestMain.cpp
copy src/{mergeFile => closestFile}/Makefile (85%)
create mode 100644 src/closestFile/closestFile.cpp
create mode 100644 src/closestFile/closestFile.h
create mode 100644 src/closestFile/closestMain.cpp
create mode 100644 src/utils/Contexts/ContextClosest.cpp
create mode 100644 src/utils/Contexts/ContextClosest.h
create mode 100644 src/utils/NewChromsweep/CloseSweep.cpp
create mode 100644 src/utils/NewChromsweep/CloseSweep.h
create mode 100644 test/bamtofastq/golden.fq
create mode 100644 test/bamtofastq/golden.fq2
create mode 100755 test/bamtofastq/test-bamtofastq.sh
create mode 100644 test/bamtofastq/test.sam
create mode 100644 test/closest/bug157_a.bed
create mode 100644 test/closest/bug157_b.bed
create mode 100644 test/closest/d.bed
create mode 100644 test/closest/d_d1F.bed
create mode 100644 test/closest/d_d1R.bed
create mode 100644 test/closest/d_d2F.bed
create mode 100644 test/closest/d_d2R.bed
create mode 100644 test/closest/d_id.bed
create mode 100644 test/closest/d_iu.bed
create mode 100644 test/closest/d_q1.bed
create mode 100644 test/closest/d_q2.bed
create mode 100644 test/closest/mdb1.bed
create mode 100644 test/closest/mdb2.bed
create mode 100644 test/closest/mdb3.bed
create mode 100644 test/closest/mq1.bed
copy test/{map/a.vsorted.bed => closest/sortAndNaming/alpha_all.bed} (58%)
create mode 100644 test/closest/sortAndNaming/alpha_missing.bed
create mode 100644 test/closest/sortAndNaming/db1_gls.bed
create mode 100644 test/closest/sortAndNaming/db1_leadingZero.txt
create mode 100644 test/closest/sortAndNaming/db1_noChr.bed
create mode 100644 test/closest/sortAndNaming/db1_num.bed
create mode 100644 test/closest/sortAndNaming/db2_num.bed
create mode 100644 test/closest/sortAndNaming/db2_numBackwards.bed
create mode 100644 test/closest/sortAndNaming/db3_numBackwards.bed
copy test/{map/a.vsorted.bed => closest/sortAndNaming/num_all.bed} (58%)
create mode 100644 test/closest/sortAndNaming/num_missing.bed
create mode 100644 test/closest/sortAndNaming/q1_gls.bed
create mode 100644 test/closest/sortAndNaming/q1_num.bed
create mode 100644 test/closest/sortAndNaming/q1a_num.bed
create mode 100644 test/closest/sortAndNaming/sdb1.bed
create mode 100644 test/closest/sortAndNaming/sq1.bed
create mode 100644 test/closest/sortAndNaming/test-sort-and-naming.sh
create mode 100644 test/closest/strand-test-c.bed
create mode 100644 test/closest/strand-test-d.bed
create mode 100644 test/fisher/README.md
create mode 100644 test/fisher/a.bed
create mode 100644 test/fisher/b.bed
create mode 100644 test/fisher/cmp.sh
create mode 100644 test/fisher/plot.py
create mode 100644 test/fisher/shuf.sh
create mode 100644 test/fisher/sim.py
create mode 100644 test/fisher/t.500.genome
create mode 100644 test/fisher/t.60.genome
create mode 100644 test/fisher/test-fisher.sh
create mode 100644 test/intersect/a_testZeroLen.bed
create mode 100644 test/intersect/a_vcfSVtest.vcf
create mode 100644 test/intersect/b_testZeroLen.bed
create mode 100644 test/intersect/b_vcfSVtest.vcf
create mode 100644 test/intersect/bug150_a.bed
create mode 100644 test/intersect/bug150_b.bed
copy test/{map/a.vsorted.bed => intersect/sortAndNaming/alpha_all.bed} (58%)
create mode 100644 test/intersect/sortAndNaming/alpha_missing.bed
create mode 100644 test/intersect/sortAndNaming/bigTests/2.21_500Kvs500K.txt
create mode 100644 test/intersect/sortAndNaming/bigTests/2.21_5v5.txt
create mode 100644 test/intersect/sortAndNaming/bigTests/2.21_chr1.txt
create mode 100644 test/intersect/sortAndNaming/bigTests/curr500Kvs500K.txt
create mode 100644 test/intersect/sortAndNaming/bigTests/curr5v5.txt
create mode 100644 test/intersect/sortAndNaming/bigTests/currChr1.txt
create mode 100644 test/intersect/sortAndNaming/bigTests/db500K.bed
create mode 100644 test/intersect/sortAndNaming/bigTests/dbchr1.bed
create mode 100644 test/intersect/sortAndNaming/bigTests/diffs.txt
create mode 100644 test/intersect/sortAndNaming/bigTests/q500K.bed
create mode 100644 test/intersect/sortAndNaming/bigTests/qchr1.bed
create mode 100644 test/intersect/sortAndNaming/db1_gls.bed
create mode 100644 test/intersect/sortAndNaming/db1_leadingZero.txt
create mode 100644 test/intersect/sortAndNaming/db1_noChr.bed
create mode 100644 test/intersect/sortAndNaming/db1_num.bed
create mode 100644 test/intersect/sortAndNaming/db2_num.bed
create mode 100644 test/intersect/sortAndNaming/db2_numBackwards.bed
create mode 100644 test/intersect/sortAndNaming/db3_numBackwards.bed
create mode 100644 test/intersect/sortAndNaming/diffs.txt
create mode 100644 test/intersect/sortAndNaming/exp1
copy test/{map/a.vsorted.bed => intersect/sortAndNaming/num_all.bed} (58%)
create mode 100644 test/intersect/sortAndNaming/num_missing.bed
create mode 100644 test/intersect/sortAndNaming/q1_gls.bed
create mode 100644 test/intersect/sortAndNaming/q1_num.bed
create mode 100644 test/intersect/sortAndNaming/q1a_num.bed
create mode 100644 test/intersect/sortAndNaming/sdb1.bed
create mode 100644 test/intersect/sortAndNaming/sq1.bed
create mode 100644 test/intersect/sortAndNaming/test-sort-and-naming.sh
create mode 100644 test/intersect/splitBug155_a.bed
create mode 100644 test/intersect/splitBug155_b.bed
delete mode 100644 test/jaccard/d.bed
create mode 100644 test/merge/expFormat.bed
create mode 100644 test/merge/precisionTest2.bed
create mode 100644 test/merge/vcfSVtest.vcf
create mode 100644 tutorial/Makefile
create mode 100644 tutorial/answers.html
create mode 100644 tutorial/answers.md
create mode 100644 tutorial/bedtools.html
create mode 100644 tutorial/bedtools.md
create mode 100644 tutorial/bootstrap.css
create mode 100644 tutorial/template.class.html
create mode 100644 tutorial/template.html
--
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