[med-svn] [bedtools] annotated tag debian/2.25.0-1 created (now fa73fd9)
Charles Plessy
plessy at moszumanska.debian.org
Fri Sep 4 15:36:55 UTC 2015
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to annotated tag debian/2.25.0-1
in repository bedtools.
at fa73fd9 (tag)
tagging 9cfdb13fa864abb6a9e0ab5b4dcee29757883013 (commit)
replaces debian/2.21.0-1
tagged by Charles Plessy
on Fri Sep 4 17:36:47 2015 +0200
- Log -----------------------------------------------------------------
bedtools (2.25.0-1) unstable; urgency=medium
e37865 Merge tag 'v2.25.0' into debian/unstable
-- Charles Plessy <plessy at debian.org> Fri, 04 Sep 2015 16:55:21 +0200
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Aaron Quinlan (41):
Merge pull request #126 from brentp/contingency-order
Merge pull request #132 from ryan-williams/fastq
Merge pull request #134 from brentp/fisher-precision
Merge pull request #139 from nkindlon/master
Merge pull request #142 from wookietreiber/wip-make-install-target
Merge pull request #143 from arjanvandervelde/patch-1
Merge pull request #146 from nkindlon/master
Merge pull request #149 from daler/master
Merge pull request #151 from tleonardi/master
Merge pull request #152 from nkindlon/master
Merge pull request #163 from nkindlon/master
Merge pull request #165 from nkindlon/master
Update README.md
Update conf.py
Merge pull request #168 from nkindlon/master
Merge pull request #170 from lindenb/master
Merge pull request #172 from lindenb/master
Merge pull request #179 from nkindlon/master
Merge pull request #190 from nkindlon/master
Merge pull request #194 from jayhesselberth/reverse-windows
Merge pull request #201 from nkindlon/master
Merge pull request #202 from nkindlon/master
Merge pull request #203 from nkindlon/master
Update README.md
Merge pull request #204 from nkindlon/master
Merge pull request #219 from lindenb/sortOnRef
Merge pull request #222 from nkindlon/master
Merge pull request #224 from nkindlon/master
Merge pull request #231 from yanlinlin82/master
Merge pull request #225 from nkindlon/master
Merge pull request #239 from nkindlon/master
Merge pull request #242 from gtamazian/getfasta-fixes
Merge pull request #243 from nkindlon/master
Merge pull request #244 from nkindlon/master
Merge pull request #245 from nkindlon/master
Merge pull request #247 from nkindlon/master
Update README.md
Update README.md
Merge pull request #261 from nkindlon/master
Merge pull request #265 from nkindlon/master
Merge pull request #249 from gtamazian/test-fixes
Andreas Tille (18):
Remove superfluous debian/README.source
Add README.source to descripe the workflow for this repository that derives from Debian Med policy
Replace specific version by "<version>"
Add policy URL with the short explanation
Further hints
Fix pritine-tar step description
Merge tag 'v2.24.0' into debian/unstable
Refresh patches
Mention new upstream version in changelog
Bash completions now go to /usr/share/bash-completion/completions
Strip executable flag from all *.bed files
Make sure all *.sh scripts of the test suite have a proper '#!/bin/bash' line and the executable flag set
update download location, turn DEP5 incompatible License field in header into a Comment
Upload to unstable
Tests need bgzip from tabix package
Add missing input file for tests and fix upstream test script
link to genomes files in autopkgtests to enable more tests passing
Fix MIPS build issue
Arjan van der Velde (1):
changed compare function to have "unsigned int"
Brent Pedersen (10):
fix #117 by re-ordering contingency table. thanks @thomasgilgenast for a clear report
better precision in reporting for fisher
tabs -> spaces
initial go at -exclude for fisher
reorganize contingency table
change fisher to use numbers of intervals rather than bases of overlap
scripts for comparing to shuffled
prevent < 0 in n21
add -m option to merge intervals
tuning, testing and docs for fisher
Charles Plessy (11):
Merge tag 'v2.22.1' into debian/unstable
New upstream release, no new copyright nor license notice.
Normalised with cme fix.
Conforms to Policy 3.9.6.
Provisional changelog.
Restore the License field in the header: Lintian is wrong.
Merge tag 'v2.25.0' into debian/unstable
Merged new upstream release.
Remove patch applied upstream.
No new copyright nor license notice.
bedtools (2.25.0-1) unstable; urgency=medium
Christian Krause (3):
adds make install target
adds CPPFLAGS to all compilation targets
Merge branch 'master' into wip-issue-206
Gaik Tamazian (5):
Tests for IUPAC processing fixed
Show warning if a FASTA index file is outdated
Test compatibility with OS X improved
OS X compatibility fix
Delete temporary files after test completion
John Marshall (3):
Move "using namespace std" after #includes
Avoid overflow in int2str()
Minor makefile improvments
Linlin Yan (1):
Fix a crash bug (when end == -1).
Neil Kindlon (92):
First check-in for new closest tool
Adding corrected Makefile
Forgot RecordOutputMgr
first check-in for new closest tool
Bug fixes and more unit tests for closest
Corrections and unit tests for closest -D option.
Fixed one more bug with tie mode resolution when using mdb's.
Including files for minor fixes omitted in yesterday's check-in
Fixed bug 100, allowing scientific notation for coords, not returning INT_MIN for invalid numbers
Fixed bug133, missing intersection of zero length records
Read VCF struct vars length from SVLEN tag instead of using length of varRef field
VcfRecord code cleanup, add intersect unit test test for VCF SV's.
added -prec option, default 10. Updated unit tests for merge, map, jaccard. Accept stdin by default in merge.
Detect differently ordered files in chromsweep and closest. Merged Fisher changes.
Correcting merge conflicts in NewChromsweep.h and .cpp
Updated jaccard unit test to reflect chromsweep change
Cleaned up error message for sort order detection of missing chrom
Fix for bug 150, closest hangs with -d and tie first mode
Added tleonardi's changes for bug 150 re: overlap bases with -split in intersect
changes for request #125: return non-zero on errors.
Bug fixes for closest and bug 155
Merge branch 'master' of https://github.com/nkindlon/bedtools2
Forgot a new test file for closest
More sort order unit tests for chromsweep and closest; bug fixes and minor enhancements
Removed large closest tests from repository
Removed test debugging files from repository
Fixed bug157: ties not prevented by -iu/-id
Fixed bug164, closest runs slower with -id
Merge branch 'master' of https://github.com/nkindlon/bedtools2
Fixed bug167: stranded chromsweep wasn't working
K closest finally working; chrom name conventions test change
addressing merge conflict
Merge branch 'master' of https://github.com/nkindlon/bedtools2
Merge remote-tracking branch 'upstream/master'
Added closest -fu and -fd, updated help
Added files
Fixing merge errors
src/utils/Contexts/ContextBase.cpp
Merge error corrections
forgot context Makefile
another merge error
yet another merge error
Cahnged Closest's RecDistList class to not use map
bug fixes for kclosest sorted output, 0 length records, and map a vs b file with multi-dbs
forgot new test files for intersect unit tests
Fixed context error that broke merge
Added first and last to help options for -o
Fixed bug for -nonamecheck, added help, unit test
Merge remote-tracking branch 'upstream/master'
Added unit test for closest to check -header option
First check-in for new version of subtract
added unit tests for -sorted and multiple databases.
Added -wb and -wo to subtract help
Addressed bug #208; seg fault when VCF doesn't have SVLEN for imprecise variants.
Changed -nonamecheck to warning only, added to help for map, closest, jaccard
Corrected bug 218 by disabling intra-file name convention checking and allowing -nonamecheck for unsorted files
Fixed bug 223, Insertions for VCF records. Added unit test.
Merge branch 'master' of https://github.com/nkindlon/bedtools2
corected unit test files for VCF insertions; changed to min instead of max for SV's with multiple vals
first check in for mass refactor from program to tools API
forgot src/utils/ToolBase directory
Forgot unit test directory for spacing.
Fixed bug where name conventions weren't tested for unsorted data; stopped namecheck on unmapped bam records
first check in for new coverage tool
Merge branch 'master' of https://www.github.com/nkindlon/bedtools2
Fixed BedPlus bug, now only requires first 3 fields instead of 6
Unit tests for coverge, corrections to -split behavior for jaccard and fisher, minor code clean up
Changed help in all tools to use common help
forgot a.bed in unit tests for coverage
forgot b.bed in coverage unit tests
Fixed sample unit test
Fixed some merge errors
Fixed build break in CommonHelp
Addressed BinTree memory blow-up; -m in fisher (w/ unit tests)
Removed accidental copy in BinTree to fix speed
Changed common help to remove -names, -filenames, and -sortout from all tools but intersect and closest.
Addressed >2 numbers in VCF SVLEN, can appear at endl w/ tab, semi-colon, newline or null
Added extra unit test for vcf svlen - single # at end of line
Changed vector copies to references
Completed #181, GFF can have extra fields. Also, SVlen in VCF takes max of more than two numbers (as opposed to min)
Merge remote-tracking branch 'upstream/master'
Added distinct_sort_num option to VectorOps for groupBy.
Added distinct_sort_num and distinct_sort_num desc to VectorOps (and groupBy) and KeyListOps. Added -delim to groupBy.
Did #147: don't print usage on errors.
Added -mean to coverage w/ unit test
Fixed Bug 254: stranded merge of BedPlus records w/ strand. Added strand to default output for stranded merge. Added and updated unit tests.
Missing file bug223_d.vcf for intersect unit test
Converted complement to PFM with merge-based approach, sorted input enforced
Fixed 44: race condition in bgzip for vcf files.
Fixed bug262: stranded map with BedPlus
1st check-in: Converted groupby to PFM
New unit tests (with bug fixes) for groupby
Pierre Lindenbaum (1):
simple algorithm when n< FOPEN_MAX
Ryan Williams (3):
add Netbeans folder “nbproject” to .gitignore
fix comment typo
fix bamToFastq skipping reads after unpaired reads
Tommaso Leonardi - farm (2):
Corrected error in reporting amount of overlap (issue #150)
Fix for issue #155
arq5x (88):
[ENH] add -prec to control decimal point precision in groupby
step must be non-zero
Merge branch 'master' of https://github.com/arq5x/bedtools2
update stable release information.
track _templates for docs
cleanup
merge conflicts
Setting Release-Version v2.22.0
doc tweaks
update docs version
restore defaukt precision in groupby
Merge branch 'master' of https://github.com/arq5x/bedtools2
add tutorial to docs
added tutorial
restore TOC
better tutorial
Merge branch 'master' of https://github.com/arq5x/bedtools2
merge conflicts. integrate @brentp's nice improvments to fisher.
Merge branch 'brentp-fisher-include'
update NewChromSweep signature to support fisher. May have conflicts with @nkindlon's upcoming changes. Will resolve then.
[BUG] Fix for issue #153. makewindows -s should not be required with -b.
Issue 123. Correct genomecov glyph. Thanks to @tdhock for the catch.
Fix for issue #145. -f was incorrectly set to 0.0 when using -labels, -intervals, or -names.
[BUG] fix for issue #140. chromosome boundaries not properly handled when slop values are negative. Thanks to @acdaugherty for the catch.
fixes to tutorial
allow closest ties that don't overlap.
fix conflict
updates to closest's docs
typo
change order
bigger font
goof in mdb -k 2 example.
updates to closest docs
Merge branch 'master' of https://github.com/arq5x/bedtools2
[DOC] update docs for closest and intersect.
update help messages.
fix tutorial makefile
Setting Release-Version v2.22.1
minor cleanup to split
added new "spacing" tool to report distances between intervals in a single file.
added note about sorted input.
right, the actual spacing code.
add missing includes
[BUG] -s is not required with -n
deprecate -abam and update help to show that -a supports BAM
formatting
Setting Release-Version v2.23.0
update docs for 2.23.0
enable -header for closest.
revcomp support for IUPAC
add tests for getfasta
Merge branch 'master' of https://github.com/arq5x/bedtools2
fix merge docs on how to report strand with . Thanks to @balwierz.
cleanup
merge cleanup
fix help to reflect interface change
merge conflicts
Merge branch 'jmarshall-warnings3'
merge conflict
only set end to 1 if slop is negative and rolls off start of chrom
tweak test
update coverage docs
update the help for coverage to reflect new role of A versus B.
add note about CLI change for coverage
update release history for 2.24.0
bump docs version
Setting Release-Version v2.24.0
formatting
typo
resolve conflict
t push origin masterMerge branch 'wookietreiber-wip-issue-206'
settle on uint32_t signature for QuickString. Resolves #267 and #271?
[BUG] fix longstanding bug where genomecov did not report chromosomes with no data at all.
Merge branch 'master' of https://github.com/arq5x/bedtools2
add vcfsort script
add support for -F and -e
missing genomecov test files
coverage does not need op columns. fixes #287
pretty split tests
missing doc images. fixes #285
add new tests for -e anf -F options
update docs for -e and -F
update history for 2.25.0
update docs version
Setting Release-Version v2.25.0
docs formatting
fix Makefile
Setting Release-Version v2.25.0
daler (1):
fix formatting of fisher table
jayhesselberth (5):
clean compile, need to test
fix param parsing; add 1 to win number
test stub; refactor num_window calculation
test stubs; ``-n`` is excepting now
all tests pass
lindenb (6):
betools pool
bedtools split
error message
moved from long to double
display double/long
sort BED on faidx file
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