[med-svn] [bedtools] annotated tag debian/2.21.0-1 created (now e394637)
Charles Plessy
plessy at moszumanska.debian.org
Tue Sep 23 10:25:33 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to annotated tag debian/2.21.0-1
in repository bedtools.
at e394637 (tag)
tagging 683546654c47740cbd431dd3b330de580ef150ff (commit)
replaces debian/2.19.1-1
tagged by Charles Plessy
on Tue Sep 23 19:25:04 2014 +0900
- Log -----------------------------------------------------------------
bedtools (2.21.0-1) unstable; urgency=medium
856a5fd Merge tag 'v2.21.0' into debian/unstable
a4f6ab7 Merge corrections on version number.
-- Charles Plessy <plessy at debian.org> Tue, 23 Sep 2014 18:48:17 +0900
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Aaron Quinlan (22):
Merge pull request #48 from Debian/suggestion-for-testsuite
Merge pull request #53 from nkindlon/master
Merge pull request #63 from lindenb/fixBlockedIntervals
Update BlockMgr.cpp
Merge pull request #64 from nkindlon/master
Merge pull request #67 from nkindlon/master
Merge pull request #68 from nkindlon/master
Merge pull request #69 from nkindlon/master
Merge pull request #75 from alexpenson/patch-1
Merge pull request #76 from nkindlon/master
Merge pull request #79 from nkindlon/master
Merge pull request #83 from nkindlon/master
Merge pull request #86 from nkindlon/master
Merge pull request #89 from mdshw5/master
Merge pull request #95 from jmarshall/warnings2
Merge pull request #94 from brentp/stats
Merge pull request #99 from brentp/sloppy
Merge pull request #108 from bioinfocoderz/patch-1
Merge pull request #107 from martijnvermaat/hg38
Merge pull request #110 from dhoeric/patch-1
Merge pull request #111 from hiberbear/patch-1
Merge pull request #112 from cinquin/master
Alex Penson (1):
Update installation.rst
Andreas Tille (10):
Add "Depends: @, samtools" as advised in #747337
Use content from bedtools-test package to actually run the test suite
Use dh to easily enable unit tests at package build time
Build-Depends: samtools to run the full test suite
Imported Upstream version 2.20.1
Merge tag '2.20.1' into debian/unstable
New upstream version
Fix permission of some genome example files
Merge branch 'debian/unstable' of ssh://git.debian.org/git/debian-med/bedtools into debian/unstable
Merge branch 'master' of ssh://git.debian.org/git/debian-med/bedtools
Brent Pedersen (3):
Fisher's Exact Test
fix slop with -pct
make sure it doesn't accumulate
Charles Plessy (8):
Merge branch 'master' into debian/unstable
Merge tag 'v2.20.1' into debian/unstable
New upstream release; no new license no copyright statement.
Merge branch 'master' of https://github.com/arq5x/bedtools2
Merge tag 'v2.21.0' into debian/unstable
Merge branch 'master' into debian/unstable
New upstream release; no new copyright nor license notices.
bedtools (2.21.0-1) unstable; urgency=medium
Eric Ho (1):
Update the format on code block
John Marshall (3):
Move "using namespace std" after #includes
Miscellaneous portability / warning fixes
Check stderr is empty, not stdout (fixes test for #46)
Martijn Vermaat (1):
Add human hg38 genome file
Matt Shirley (1):
Update links in docs to point to the bedtools2 github pages.
Olivier Cinquin (1):
Allow compilation with FreeBSD/clang.
arq5x (34):
[DOC] add new usage examples from the wild
[DOC] add new usage examples from the wild
tweak README
remove extraneous header tab
fix most filetype issues. intersect still raises error with empty files.
[ENH] all shuffle with -incl to follow data distribution
[TST] run shuffle tests.
allow merge -d to have negative values for minimum overlap.
add missing help menu items (-S -header) to merge
cleanup KeyListOps help formatting
cleanup unit tests.
allow command line includes for make
[DOC] fix formatting for unionbedg
[DOC] fix formatting for unionbedg
correct intersect unit test - was pointing to test binary
tweaks for 2.20.0
Setting Release-Version v2.20.0
docs formatting
fix for slop bug in issue \#82
updates for 2.20.1
update history for 2.20.1
Setting Release-Version v2.20.1
adjust Makefile to accomodate Intel compiler.
Merge branch 'master' of https://github.com/arq5x/bedtools2
add @brentp's fisher tool to the help menu.
fix merge conflicts
[DOC] remove sticky note from docs. general hatred.
update fisher to use RecordKeyVector
logo:
update release history
update docs and figures for multi-db intersect
Setting Release-Version v2.21.0
[DOC] typo
latest=2.21.0
bioinfocoderz (1):
Update overview.rst
lindenb (1):
support for operators 'X' and '=' in method BlockedIntervals.cpp/GetBamBlocks
nkindlon (33):
Merge converted to PFM, first check-in
Handling empty files with headers
Merge remote-tracking branch 'upstream/master' into merge
Merge branch 'master' of https://github.com/nkindlon/bedtools2
Fixed merge conflicts
Unit tests and bug fixes for merge release
Merge branch 'merge'
Final unit tests for merge, including stranded merge bug fixes.
Merge branch 'merge'
Test commit
merge bug fixes and unit tests
Made Merge only print Bed3 output for BAM, added unit test
Added jaccard w/ -split and unit tests. Fixed Bam input as bam output bug, added unit test in sample.
Added stranded info to jaccard and merge help, fixed stranded jaccard bug
added changes to stop CLANG compiler warnings.
Added unit test to merge to confirm precision
Allowed numeric ops for non-numeric columns
Updated map's unit test for allowance of numeric ops on non-num cols
Stripped whitespace and DOS endLine chars in parsing.
Fixed map and merge help messages.
Changes fetch columns by number from BAM files.
Resolved merge conflicts with KeyListOps.cpp, test-merge.sh, and test-map.sh
More unit tests for column ops on BAM
Fixed bug for files with no newlines.
Added new -iobuf option and unit tests.
First check-in for multi-sweep
Multiple DB intersect support with unit tests and updated help messages.
Corrected merge conflicts
Corrected errors caused during merge-conflict resolution
Changes for multi-DB intersection.
merge conflict corrections
fixing merge errors, again.
Stop Chromsweeep cache scan when DB is after query; allow BAM unmapped reads/chrom in genome file.
shao (1):
Update intersect.rst
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