[med-svn] [bedtools] branch debian/unstable updated (b4fa8e1 -> 883e83f)
Charles Plessy
plessy at moszumanska.debian.org
Fri Mar 21 07:23:46 UTC 2014
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plessy pushed a change to branch debian/unstable
in repository bedtools.
from b4fa8e1 Move debian/upstream to debian/upstream/metadata
adds 77c1bda Created new KeyListOps class to replace vectorOps. Converted map tool to this.
adds 4793c98 Merge pull request #39 from nkindlon/master
adds 2268ee4 Refactored KeyListOps, Context, mapFile for KeyListOps re-usability by other tools.
adds 8bba882 forgot main Makefile update.
adds af1113e More unit tests, also fixed files messed up by previous merge attempt.
adds 1a0737d Merge pull request #41 from nkindlon/master
adds a70cc30 added: mm10 mouse genome
adds 8be6539 Merge pull request #40 from theoryno3/master
adds 9509809 Fixed intersect bug so that bed query with Bam DB correctly gives bed output. Added unit test.
adds 733c84b Merge pull request #43 from nkindlon/master
adds 5032438 [DOC] multiple ops/cols allowed in a single map run. also, speed comparo.
adds 3719038 Setting Release-Version v2.19.1
adds 732f683 Setting Release-Version v2.19.1
adds a3fefa2 Setting Release-Version v2.19.1
new 479e63b Merge tag 'v2.19.1' into debian/unstable
new c6fb02a New upstream release; no new copyright nor license statements.
new 164028e Merge branch 'debian/unstable' of git+ssh://git.debian.org/git/debian-med/bedtools into debian/unstable
new 8082020 Fixed slop bug when slop factor exceeds MAX signed int.
new dc51d7d Merge pull request #47 from nkindlon/master
new 6fbc3c2 just peak at first bit in isGzipFile() fix for issue46
new c1fb7ab Call bedtools via the BT variable, allowing to override the location.
new b9c717e Access data via a DATA variable, allowing to override the location.
new 05807b3 Merge branch 'suggestion-for-testsuite' into debian/unstable
new 93a7cf1 Create autopkgtest testsuite and a new package bedtools-test.
new 4fd441a Removed exception of compression now that test files have been moved.
new 46183f8 Update path, correct license short name.
new 883e83f bedtools (2.19.1-1) unstable; urgency=medium
The 13 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:
Makefile | 1 +
debian/bedtools-test.install | 3 +
debian/{docs => bedtools.docs} | 0
debian/{install => bedtools.install} | 1 -
debian/changelog | 14 +
debian/control | 11 +
debian/copyright | 10 +-
debian/rules | 2 -
debian/tests/control | 1 +
debian/tests/upstream | 21 ++
.../images/tool-glyphs/map-speed-comparo.png | Bin 0 -> 41233 bytes
docs/content/tools/map.rst | 35 +-
genomes/mouse.mm10.genome.txt | 66 ++++
src/intersectFile/Makefile | 1 +
src/mapFile/Makefile | 1 +
src/mapFile/mapFile.cpp | 67 +---
src/mapFile/mapFile.h | 85 +----
src/mapFile/mapMain.cpp | 138 --------
src/nekSandbox1/Makefile | 1 +
src/regressTest/Makefile | 1 +
src/sampleFile/Makefile | 1 +
src/slopBed/slopBed.cpp | 30 +-
src/slopBed/slopBed.h | 2 +-
src/utils/BinTree/Makefile | 1 +
src/utils/Contexts/ContextBase.cpp | 132 +++++++-
src/utils/Contexts/ContextBase.h | 21 +-
src/utils/Contexts/ContextIntersect.h | 2 +
src/utils/Contexts/ContextMap.cpp | 93 +-----
src/utils/Contexts/ContextMap.h | 20 +-
src/utils/Contexts/Makefile | 1 +
src/utils/FileRecordTools/Records/BamRecord.cpp | 5 +
src/utils/FileRecordTools/Records/BamRecord.h | 1 +
.../FileRecordTools/Records/Bed12Interval.cpp | 26 ++
src/utils/FileRecordTools/Records/Bed12Interval.h | 1 +
src/utils/FileRecordTools/Records/Bed3Interval.cpp | 20 ++
src/utils/FileRecordTools/Records/Bed3Interval.h | 2 +
src/utils/FileRecordTools/Records/Bed4Interval.cpp | 5 +
src/utils/FileRecordTools/Records/Bed4Interval.h | 1 +
src/utils/FileRecordTools/Records/Bed5Interval.cpp | 13 +
src/utils/FileRecordTools/Records/Bed5Interval.h | 1 +
src/utils/FileRecordTools/Records/Bed6Interval.cpp | 17 +
src/utils/FileRecordTools/Records/Bed6Interval.h | 1 +
.../FileRecordTools/Records/BedGraphInterval.cpp | 11 +
.../FileRecordTools/Records/BedGraphInterval.h | 1 +
.../FileRecordTools/Records/BedPlusInterval.cpp | 15 +
.../FileRecordTools/Records/BedPlusInterval.h | 2 +
src/utils/FileRecordTools/Records/GffRecord.cpp | 36 ++
src/utils/FileRecordTools/Records/GffRecord.h | 1 +
src/utils/FileRecordTools/Records/Record.cpp | 6 +-
src/utils/FileRecordTools/Records/Record.h | 2 +
src/utils/GenomeFile/Makefile | 1 +
src/utils/KeyListOps/KeyListOps.cpp | 364 ++++++++++++++++++++
src/utils/KeyListOps/KeyListOps.h | 54 +++
src/utils/KeyListOps/KeyListOpsMethods.cpp | 368 +++++++++++++++++++++
src/utils/KeyListOps/KeyListOpsMethods.h | 113 +++++++
src/utils/{NewChromsweep => KeyListOps}/Makefile | 12 +-
src/utils/NewChromsweep/Makefile | 1 +
src/utils/RecordOutputMgr/Makefile | 1 +
src/utils/fileType/fileType.cpp | 25 +-
src/utils/general/Makefile | 2 +-
src/utils/general/QuickString.cpp | 65 ++++
src/utils/general/QuickString.h | 19 ++
src/utils/version/version_release.txt | 6 +-
test/intersect/test-intersect.sh | 11 +-
test/map/test-map.sh | 148 +++++++--
test/reldist/test-reldist.sh | 15 +-
test/slop/test-slop.sh | 14 +-
67 files changed, 1674 insertions(+), 474 deletions(-)
create mode 100644 debian/bedtools-test.install
rename debian/{docs => bedtools.docs} (100%)
rename debian/{install => bedtools.install} (73%)
create mode 100644 debian/tests/control
create mode 100755 debian/tests/upstream
create mode 100644 docs/content/images/tool-glyphs/map-speed-comparo.png
create mode 100644 genomes/mouse.mm10.genome.txt
create mode 100644 src/utils/KeyListOps/KeyListOps.cpp
create mode 100644 src/utils/KeyListOps/KeyListOps.h
create mode 100644 src/utils/KeyListOps/KeyListOpsMethods.cpp
create mode 100644 src/utils/KeyListOps/KeyListOpsMethods.h
copy src/utils/{NewChromsweep => KeyListOps}/Makefile (81%)
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