[med-svn] [bedtools] branch master updated (b36ce1a -> 32c26d8)
Charles Plessy
plessy at moszumanska.debian.org
Mon Jan 5 01:04:08 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 b36ce1a Merge branch 'master' of https://github.com/arq5x/bedtools2
new a60ae74 restore defaukt precision in groupby
new e7379ae adds make install target
new 0292f31 Merge pull request #142 from wookietreiber/wip-make-install-target
new 5f91a5b changed compare function to have "unsigned int"
new 5926946 Merge pull request #143 from arjanvandervelde/patch-1
new 296866f Merge branch 'master' of https://github.com/arq5x/bedtools2
new 418e5d9 add tutorial to docs
new a52fee4 added tutorial
new f542c99 restore TOC
new 39cec40 better tutorial
new 3b5afaf added -prec option, default 10. Updated unit tests for merge, map, jaccard. Accept stdin by default in merge.
new 4c6a312 Merge pull request #146 from nkindlon/master
new 2480322 Merge branch 'master' of https://github.com/arq5x/bedtools2
new 89805de fix formatting of fisher table
new fc7d185 Merge pull request #149 from daler/master
new e1f71df initial go at -exclude for fisher
new a277bba reorganize contingency table
new d6544e0 change fisher to use numbers of intervals rather than bases of overlap
new c3ab3d1 scripts for comparing to shuffled
new 3594e98 prevent < 0 in n21
new 548bcae add -m option to merge intervals
new ed4e8a9 tuning, testing and docs for fisher
new cf911bf merge conflicts. integrate @brentp's nice improvments to fisher.
new 205db6a Merge branch 'brentp-fisher-include'
new 6ae9016 update NewChromSweep signature to support fisher. May have conflicts with @nkindlon's upcoming changes. Will resolve then.
new 0f4652d [BUG] Fix for issue #153. makewindows -s should not be required with -b.
new dabde35 Issue 123. Correct genomecov glyph. Thanks to @tdhock for the catch.
new e63d83e Fix for issue #145. -f was incorrectly set to 0.0 when using -labels, -intervals, or -names.
new b7ceea4 [BUG] fix for issue #140. chromosome boundaries not properly handled when slop values are negative. Thanks to @acdaugherty for the catch.
new 92b9249 fixes to tutorial
new 90af6a7 allow closest ties that don't overlap.
new 1db6b68 Corrected error in reporting amount of overlap (issue #150)
new 49a3598 Fix for issue #155
new d8e5ba5 Merge pull request #151 from tleonardi/master
new 4c7213c Detect differently ordered files in chromsweep and closest. Merged Fisher changes.
new 758cd6a Correcting merge conflicts in NewChromsweep.h and .cpp
new b561a2f Updated jaccard unit test to reflect chromsweep change
new a2cacdf Cleaned up error message for sort order detection of missing chrom
new d819c40 Fix for bug 150, closest hangs with -d and tie first mode
new b70b6ca Added tleonardi's changes for bug 150 re: overlap bases with -split in intersect
new 436e6f4 Bug fixes for closest and bug 155
new 50ae752 changes for request #125: return non-zero on errors.
new cf21ba5 Merge branch 'master' of https://github.com/nkindlon/bedtools2
new 2a2ae0c Forgot a new test file for closest
new 4422985 More sort order unit tests for chromsweep and closest; bug fixes and minor enhancements
new e94c559 Removed large closest tests from repository
new 2661889 Removed test debugging files from repository
new 7fd03d3 Merge pull request #152 from nkindlon/master
new effc83e Fixed bug157: ties not prevented by -iu/-id
new b3bcab1 Merge pull request #163 from nkindlon/master
new d736f16 fix conflict
new ab663c4 updates to closest's docs
new e194c15 typo
new 823a1fc change order
new 9fdb22f bigger font
new df4e52b goof in mdb -k 2 example.
new 042294d updates to closest docs
new 4983727 Fixed bug164, closest runs slower with -id
new 6744fd0 Merge pull request #165 from nkindlon/master
new a6e1ecb Merge branch 'master' of https://github.com/arq5x/bedtools2
new 330bfb5 [DOC] update docs for closest and intersect.
new 4119372 update help messages.
new 60111a3 fix tutorial makefile
new a596d5a Setting Release-Version v2.22.1
new 2d8c5a4 Update README.md
new 2f4d319 Update conf.py
new 32c26d8 Merge branch 'master' of https://github.com/arq5x/bedtools2
The 67 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 | 1 +
Makefile | 8 +
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 | 448 +-
docs/content/tools/fisher.rst | 94 +-
docs/content/tools/intersect.rst | 369 +-
docs/index.rst | 11 +-
src/closestFile/closestFile.cpp | 4 +
src/closestFile/closestMain.cpp | 7 +-
src/fisher/Fisher.cpp | 71 +-
src/fisher/Fisher.h | 9 +
src/fisher/Makefile | 35 +-
src/fisher/fisherMain.cpp | 11 +-
src/groupBy/groupBy.cpp | 2 +-
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 | 117 +-
src/utils/Contexts/ContextBase.h | 23 +-
src/utils/Contexts/ContextClosest.cpp | 2 +-
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/FileRecordTools/Records/BlockMgr.cpp | 7 +-
src/utils/FileRecordTools/Records/Record.cpp | 32 +
src/utils/FileRecordTools/Records/Record.h | 4 +
src/utils/KeyListOps/KeyListOps.cpp | 29 +-
src/utils/KeyListOps/KeyListOps.h | 6 +
src/utils/NewChromsweep/CloseSweep.cpp | 209 +-
src/utils/NewChromsweep/CloseSweep.h | 14 +-
src/utils/NewChromsweep/NewChromsweep.cpp | 251 +-
src/utils/NewChromsweep/NewChromsweep.h | 44 +-
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 22 +-
src/utils/bedFile/bedFile.cpp | 18 +-
src/utils/bedFile/bedFile.h | 1 +
src/utils/general/ParseTools.h | 8 +-
src/utils/version/version_release.txt | 6 +-
src/windowMaker/windowMakerMain.cpp | 2 +-
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_id.bed | 2 +
test/closest/d_iu.bed | 2 +
.../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 | 135 +-
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/b_testZeroLen.bed | 1 -
test/intersect/bug150_a.bed | 1 +
test/intersect/bug150_b.bed | 2 +
test/intersect/new_test-intersect.sh | 9 +-
.../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/precisionTest2.bed | 5 +
test/merge/test-merge.sh | 40 +
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 +
143 files changed, 1153895 insertions(+), 566 deletions(-)
create mode 100644 docs/content/images/fisher/res-genes.png
create mode 100644 docs/content/images/tool-glyphs/closest-glyph.png
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_id.bed
create mode 100644 test/closest/d_iu.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/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/precisionTest2.bed
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
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