[med-svn] [bedtools] branch master updated (69e2731 -> b36ce1a)
Charles Plessy
plessy at moszumanska.debian.org
Wed Nov 12 04:54:21 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository bedtools.
from 69e2731 Merge branch 'master' of https://github.com/arq5x/bedtools2
new 51ef360 fix #117 by re-ordering contingency table. thanks @thomasgilgenast for a clear report
new c7c9078 Merge pull request #126 from brentp/contingency-order
new 479a2fc [ENH] add -prec to control decimal point precision in groupby
new 15b2539 step must be non-zero
new 4c0dd78 add Netbeans folder “nbproject” to .gitignore
new 21f53b7 fix comment typo
new 41f96cf fix bamToFastq skipping reads after unpaired reads
new 62802ec Merge pull request #132 from ryan-williams/fastq
new f1d7c76 better precision in reporting for fisher
new a5bd6db tabs -> spaces
new e6f1418 Merge pull request #134 from brentp/fisher-precision
new 81d2ada Merge branch 'master' of https://github.com/arq5x/bedtools2
new 1b707ee update stable release information.
new 13e4308 track _templates for docs
new 5b47f91 cleanup
new 54e27a1 First check-in for new closest tool
new 8cc9c0a Adding corrected Makefile
new 34f0dd7 Forgot RecordOutputMgr
new 897d1a8 first check-in for new closest tool
new 8a2e369 Bug fixes and more unit tests for closest
new 5d20ecf Corrections and unit tests for closest -D option.
new 267cb42 Fixed one more bug with tie mode resolution when using mdb's.
new 7b2a560 Including files for minor fixes omitted in yesterday's check-in
new 31878f3 merge conflicts
new 5ba347e Fixed bug 100, allowing scientific notation for coords, not returning INT_MIN for invalid numbers
new 0ea1769 Fixed bug133, missing intersection of zero length records
new 0b8612d Read VCF struct vars length from SVLEN tag instead of using length of varRef field
new 858cc4b VcfRecord code cleanup, add intersect unit test test for VCF SV's.
new 2f90e6a Merge pull request #139 from nkindlon/master
new 85f5a10 Setting Release-Version v2.22.0
new e0fdbbf doc tweaks
new 91928cf update docs version
new b36ce1a Merge branch 'master' of https://github.com/arq5x/bedtools2
The 33 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 | 4 +
Makefile | 2 +-
README.md | 2 +-
docs/conf.py | 4 +-
docs/content/tools/closest.rst | 9 +
docs/content/tools/fisher.rst | 6 +-
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 | 41 +
src/closestFile/closestFile.h | 31 +
src/closestFile/closestMain.cpp | 107 +++
src/fisher/Fisher.cpp | 116 ++-
src/groupBy/groupBy.cpp | 55 +-
src/utils/Contexts/ContextBase.cpp | 2 +-
src/utils/Contexts/ContextClosest.cpp | 222 +++++
src/utils/Contexts/ContextClosest.h | 65 ++
src/utils/Contexts/Makefile | 10 +-
.../FileReaders/SingleLineDelimTextFileReader.cpp | 17 +
.../FileReaders/SingleLineDelimTextFileReader.h | 12 +
src/utils/FileRecordTools/Records/Record.cpp | 14 +-
src/utils/FileRecordTools/Records/VcfRecord.cpp | 24 +-
src/utils/FileRecordTools/Records/VcfRecord.h | 2 +-
src/utils/NewChromsweep/CloseSweep.cpp | 426 +++++++++
src/utils/NewChromsweep/CloseSweep.h | 53 ++
src/utils/NewChromsweep/Makefile | 80 +-
src/utils/NewChromsweep/NewChromsweep.cpp | 506 ++++++-----
src/utils/NewChromsweep/NewChromsweep.h | 24 +-
src/utils/RecordOutputMgr/Makefile | 78 +-
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 972 +++++++++++----------
src/utils/RecordOutputMgr/RecordOutputMgr.h | 148 ++--
src/utils/general/ParseTools.cpp | 29 +-
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/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_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 +
test/closest/test-closest.sh | 400 ++++++++-
test/intersect/a_testZeroLen.bed | 3 +
test/intersect/a_vcfSVtest.vcf | 5 +
test/intersect/b_testZeroLen.bed | 3 +
test/intersect/b_vcfSVtest.vcf | 5 +
test/intersect/new_test-intersect.sh | 50 ++
test/merge/expFormat.bed | 1 +
test/merge/test-merge.sh | 24 +
test/merge/vcfSVtest.vcf | 5 +
61 files changed, 2690 insertions(+), 1684 deletions(-)
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/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_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
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/merge/expFormat.bed
create mode 100644 test/merge/vcfSVtest.vcf
--
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