[med-svn] [bedtools] branch debian/unstable updated (68dfd72 -> dc2a4a4)
Charles Plessy
plessy at moszumanska.debian.org
Sat May 24 13:36:48 UTC 2014
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch debian/unstable
in repository bedtools.
from 68dfd72 Build-Depends: samtools to run the full test suite
adds e7f41f5 [DOC] add new usage examples from the wild
adds 9e50ca3 tweak README
adds 377f1b1 remove extraneous header tab
adds ed71c8e fix most filetype issues. intersect still raises error with empty files.
adds 4642a14 [ENH] all shuffle with -incl to follow data distribution
adds bcbd75b [TST] run shuffle tests.
adds f36d6db Merge converted to PFM, first check-in
adds 8b6ed4b Merge branch 'master' of https://github.com/nkindlon/bedtools2
adds fe5ea0e Handling empty files with headers
adds eb2f614 Merge remote-tracking branch 'upstream/master' into merge
adds 8284c92 Fixed merge conflicts
adds 5eb3b68 Unit tests and bug fixes for merge release
adds 9eb4337 Merge branch 'merge'
adds 1b866b6 Final unit tests for merge, including stranded merge bug fixes.
adds 3b04625 Merge branch 'merge'
adds fccfbfb Merge pull request #53 from nkindlon/master
adds d0fe42c allow merge -d to have negative values for minimum overlap.
adds 4fd41ae add missing help menu items (-S -header) to merge
adds c5d1e72 cleanup KeyListOps help formatting
adds 17ec9aa cleanup unit tests.
adds 57ce8d4 allow command line includes for make
adds fd7becf support for operators 'X' and '=' in method BlockedIntervals.cpp/GetBamBlocks
adds ba984f3 Merge pull request #63 from lindenb/fixBlockedIntervals
adds 70345fd Update BlockMgr.cpp
adds 4ef1d94 Test commit
adds b740bbf merge bug fixes and unit tests
adds bbda1f4 Made Merge only print Bed3 output for BAM, added unit test
adds e2be078 Added jaccard w/ -split and unit tests. Fixed Bam input as bam output bug, added unit test in sample.
adds 39fffc9 Added stranded info to jaccard and merge help, fixed stranded jaccard bug
adds e866785 added changes to stop CLANG compiler warnings.
adds be32e1c Added unit test to merge to confirm precision
adds 952140c Changes fetch columns by number from BAM files.
adds d42edc9 Merge pull request #64 from nkindlon/master
adds 77fae72 Merge pull request #67 from nkindlon/master
adds 3f03f6d [DOC] fix formatting for unionbedg
adds aece1e8 [DOC] fix formatting for unionbedg
adds 656fd84 Merge pull request #68 from nkindlon/master
adds 0b41d1a Merge pull request #69 from nkindlon/master
adds 143be5d Update installation.rst
adds 502c94d Merge pull request #75 from alexpenson/patch-1
adds 9ee6bac Allowed numeric ops for non-numeric columns
adds 47a801b Updated map's unit test for allowance of numeric ops on non-num cols
adds 2ae5c07 Stripped whitespace and DOS endLine chars in parsing.
adds d358798 Fixed map and merge help messages.
adds 44c8771 Merge pull request #76 from nkindlon/master
adds 9e886b4 Resolved merge conflicts with KeyListOps.cpp, test-merge.sh, and test-map.sh
adds bc90a1a More unit tests for column ops on BAM
adds f7fc153 Merge pull request #79 from nkindlon/master
adds 69eb4ea correct intersect unit test - was pointing to test binary
adds 47c6a2e tweaks for 2.20.0
adds 0cd7017 Setting Release-Version v2.20.0
adds 364f619 docs formatting
adds 4a5fc54 fix for slop bug in issue \#82
adds 18eb97a updates for 2.20.1
adds d8c6201 Fixed bug for files with no newlines.
adds 2c9675e Merge pull request #83 from nkindlon/master
adds fa9ab3b update history for 2.20.1
adds 4122ba1 Setting Release-Version v2.20.1
new 7b6b2d6 Merge tag 'v2.20.1' into debian/unstable
new dc2a4a4 New upstream release; no new license no copyright statement.
The 2 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 | 7 +-
README.md | 4 +-
RELEASE_HISTORY | 7 +
debian/changelog | 6 +
debian/copyright | 2 +-
docs/conf.py | 6 +-
RELEASE_HISTORY => docs/content/history.rst | 482 +++++-----
docs/content/installation.rst | 2 +-
docs/content/tools/jaccard.rst | 3 +
docs/content/tools/map.rst | 2 -
docs/content/tools/merge.rst | 169 ++--
docs/content/tools/unionbedg.rst | 28 +-
docs/index.rst | 3 +-
src/intersectFile/intersectFile.cpp | 3 +-
src/jaccard/Jaccard.cpp | 94 ++
src/{mapFile/mapFile.h => jaccard/Jaccard.h} | 38 +-
src/jaccard/Makefile | 29 +-
src/jaccard/jaccard.cpp | 110 ---
src/jaccard/jaccard.h | 70 --
src/jaccard/jaccardMain.cpp | 240 +++--
src/mapFile/mapFile.h | 1 -
src/mapFile/mapMain.cpp | 18 +-
src/mergeBed/Makefile | 35 -
src/mergeBed/mergeBed.cpp | 359 -------
src/mergeBed/mergeBed.h | 72 --
src/mergeBed/mergeMain.cpp | 184 ----
src/{intersectFile => mergeFile}/Makefile | 14 +-
src/mergeFile/mergeFile.cpp | 39 +
.../complementBed.h => mergeFile/mergeFile.h} | 40 +-
src/mergeFile/mergeMain.cpp | 80 ++
src/nekSandbox1/nekSandboxMain.cpp | 6 +-
src/nucBed/nucBed.cpp | 6 +-
src/sampleFile/SampleFile.cpp | 2 +-
src/shuffleBed/shuffleBed.cpp | 51 +-
src/shuffleBed/shuffleBedMain.cpp | 2 -
src/slopBed/slopBed.cpp | 34 +-
src/utils/BamTools/src/api/BamAlignment.h | 2 +-
src/utils/BamTools/src/api/SamHeader.h | 4 +-
.../src/api/internal/io/TcpSocketEngine_p.h | 2 +-
.../src/api/internal/sam/SamHeaderValidator_p.h | 4 +-
src/utils/BinTree/BinTree.cpp | 9 +-
src/utils/BlockedIntervals/BlockedIntervals.cpp | 6 +-
src/utils/Contexts/ContextBase.cpp | 66 +-
src/utils/Contexts/ContextBase.h | 47 +-
src/utils/Contexts/ContextJaccard.cpp | 109 +++
src/utils/Contexts/ContextJaccard.h | 25 +
src/utils/Contexts/ContextMap.cpp | 10 -
src/utils/Contexts/ContextMap.h | 5 -
src/utils/Contexts/ContextMerge.cpp | 176 ++++
src/utils/Contexts/ContextMerge.h | 31 +
src/utils/Contexts/Makefile | 9 +-
.../FileRecordTools/FileReaders/BamFileReader.cpp | 10 +
.../FileRecordTools/FileReaders/BamFileReader.h | 4 +-
.../FileReaders/BufferedStreamMgr.cpp | 30 +-
.../FileRecordTools/FileReaders/InputStreamMgr.cpp | 21 +-
.../FileRecordTools/FileReaders/InputStreamMgr.h | 7 +-
.../FileReaders/SingleLineDelimTextFileReader.cpp | 6 +-
src/utils/FileRecordTools/FileRecordMergeMgr.cpp | 217 +++++
src/utils/FileRecordTools/FileRecordMergeMgr.h | 58 ++
src/utils/FileRecordTools/FileRecordMgr.cpp | 186 +---
src/utils/FileRecordTools/FileRecordMgr.h | 79 +-
src/utils/FileRecordTools/Makefile | 10 +-
src/utils/FileRecordTools/Records/BamRecord.cpp | 209 ++--
src/utils/FileRecordTools/Records/BamRecord.h | 27 +-
src/utils/FileRecordTools/Records/BlockMgr.cpp | 16 +-
src/utils/FileRecordTools/Records/BlockMgr.h | 3 +
src/utils/FileRecordTools/Records/EmptyRecord.cpp | 34 +
src/utils/FileRecordTools/Records/EmptyRecord.h | 30 +
src/utils/FileRecordTools/Records/Makefile | 12 +-
src/utils/FileRecordTools/Records/Record.h | 5 +-
src/utils/FileRecordTools/Records/RecordMgr.cpp | 24 +
src/utils/FileRecordTools/Records/RecordMgr.h | 1 +
src/utils/FileRecordTools/Records/StrandQueue.cpp | 131 +++
src/utils/FileRecordTools/Records/StrandQueue.h | 47 +
.../FileRecordTools/Records/recordsTar.tar.gz | Bin 54443 -> 0 bytes
src/utils/GenomeFile/NewGenomeFile.cpp | 12 +-
src/utils/KeyListOps/KeyListOps.cpp | 142 ++-
src/utils/KeyListOps/KeyListOps.h | 20 +
src/utils/KeyListOps/KeyListOpsMethods.cpp | 21 +-
src/utils/KeyListOps/KeyListOpsMethods.h | 13 +-
src/utils/NewChromsweep/NewChromsweep.cpp | 10 +-
src/utils/RecordOutputMgr/RecordOutputMgr.cpp | 34 +-
src/utils/RecordOutputMgr/RecordOutputMgr.h | 1 +
src/utils/bedFile/bedFile.cpp | 14 +
src/utils/bedFile/bedFile.h | 4 +
src/utils/fileType/FileRecordTypeChecker.cpp | 56 +-
src/utils/fileType/FileRecordTypeChecker.h | 19 +-
src/utils/fileType/fileType.cpp | 2 +-
src/utils/general/DualQueue.h | 124 ---
src/utils/general/Makefile | 6 +-
src/utils/general/ParseTools.cpp | 34 +-
src/utils/general/ParseTools.h | 4 +-
src/utils/general/QuickString.h | 1 +
src/utils/general/Tokenizer.cpp | 102 ++
src/utils/general/Tokenizer.h | 57 ++
src/utils/version/version_release.txt | 6 +-
test/general/test-general.sh | 204 +++-
test/intersect/dosLineCharWithExtraTab_b.bed | 4 +
test/intersect/dosLineChar_a.bed | 3 +
test/intersect/headerOnly.vcf | 121 +++
test/intersect/new_test-intersect.sh | 104 +-
test/intersect/oneRecordNoNewline.bed | 1 +
test/jaccard/a.bam | Bin 0 -> 1796 bytes
test/jaccard/aMixedStrands.bed | 12 +
test/jaccard/bMixedStrands.bed | 6 +
test/{intersect/d.bed => jaccard/e.bed} | 0
test/jaccard/test-jaccard.sh | 82 +-
test/{intersect => jaccard}/three_blocks_match.bam | Bin
test/{coverage => jaccard}/three_blocks_match.bed | 0
test/map/d.bed | 2 +
test/map/fullFields.bam | Bin 0 -> 25813 bytes
test/map/test-map.sh | 44 +-
test/merge/a.full.bam | Bin 0 -> 1836 bytes
test/merge/a.gff | 6 +
test/merge/b.bed | 7 +
test/merge/bamCol10Collapse.txt | 112 +++
test/merge/bamCol11Collapse.txt | 112 +++
test/merge/bamCol1Collapse.txt | 112 +++
test/merge/bamCol3Collapse.txt | 112 +++
test/merge/bamCol4Mean.txt | 112 +++
test/merge/bamCol5Mean.txt | 112 +++
test/merge/bamCol6Collapse.txt | 112 +++
test/merge/bamCol7Collapse.txt | 112 +++
test/merge/bamCol8Mean.txt | 112 +++
test/merge/bamCol9Mean.txt | 112 +++
test/merge/fullFields.bam | Bin 0 -> 25813 bytes
test/merge/mergeBugTest.bed | 12 +
test/merge/mixedStrands.bed | 12 +
test/merge/precisionTest.bed | 10 +
test/merge/test-merge.sh | 391 ++++++--
test/merge/testA.vcf | 129 +++
test/merge/unsorted.bed | 7 +
test/sample/test-sample.sh | 11 +-
test/shuffle/excl.bed | 9 +
test/shuffle/incl.bed | 9 +
test/shuffle/simrep.bed | 1000 ++++++++++++++++++++
test/shuffle/test-shuffle.sh | 127 +++
test/slop/test-slop.sh | 21 +
test/test.sh | 3 +
139 files changed, 5910 insertions(+), 2149 deletions(-)
copy RELEASE_HISTORY => docs/content/history.rst (73%)
create mode 100644 src/jaccard/Jaccard.cpp
copy src/{mapFile/mapFile.h => jaccard/Jaccard.h} (50%)
delete mode 100644 src/jaccard/jaccard.cpp
delete mode 100644 src/jaccard/jaccard.h
delete mode 100644 src/mergeBed/Makefile
delete mode 100644 src/mergeBed/mergeBed.cpp
delete mode 100644 src/mergeBed/mergeBed.h
delete mode 100644 src/mergeBed/mergeMain.cpp
copy src/{intersectFile => mergeFile}/Makefile (81%)
create mode 100644 src/mergeFile/mergeFile.cpp
copy src/{complementBed/complementBed.h => mergeFile/mergeFile.h} (53%)
create mode 100644 src/mergeFile/mergeMain.cpp
create mode 100644 src/utils/Contexts/ContextJaccard.cpp
create mode 100644 src/utils/Contexts/ContextJaccard.h
create mode 100644 src/utils/Contexts/ContextMerge.cpp
create mode 100644 src/utils/Contexts/ContextMerge.h
create mode 100644 src/utils/FileRecordTools/FileRecordMergeMgr.cpp
create mode 100644 src/utils/FileRecordTools/FileRecordMergeMgr.h
create mode 100644 src/utils/FileRecordTools/Records/EmptyRecord.cpp
create mode 100644 src/utils/FileRecordTools/Records/EmptyRecord.h
create mode 100644 src/utils/FileRecordTools/Records/StrandQueue.cpp
create mode 100644 src/utils/FileRecordTools/Records/StrandQueue.h
delete mode 100644 src/utils/FileRecordTools/Records/recordsTar.tar.gz
delete mode 100644 src/utils/general/DualQueue.h
create mode 100644 src/utils/general/Tokenizer.cpp
create mode 100644 src/utils/general/Tokenizer.h
create mode 100644 test/intersect/dosLineCharWithExtraTab_b.bed
create mode 100644 test/intersect/dosLineChar_a.bed
create mode 100644 test/intersect/headerOnly.vcf
create mode 100644 test/intersect/oneRecordNoNewline.bed
create mode 100644 test/jaccard/a.bam
create mode 100644 test/jaccard/aMixedStrands.bed
create mode 100644 test/jaccard/bMixedStrands.bed
copy test/{intersect/d.bed => jaccard/e.bed} (100%)
copy test/{intersect => jaccard}/three_blocks_match.bam (100%)
copy test/{coverage => jaccard}/three_blocks_match.bed (100%)
create mode 100644 test/map/d.bed
create mode 100644 test/map/fullFields.bam
create mode 100644 test/merge/a.full.bam
create mode 100644 test/merge/a.gff
create mode 100644 test/merge/b.bed
create mode 100644 test/merge/bamCol10Collapse.txt
create mode 100644 test/merge/bamCol11Collapse.txt
create mode 100644 test/merge/bamCol1Collapse.txt
create mode 100644 test/merge/bamCol3Collapse.txt
create mode 100644 test/merge/bamCol4Mean.txt
create mode 100644 test/merge/bamCol5Mean.txt
create mode 100644 test/merge/bamCol6Collapse.txt
create mode 100644 test/merge/bamCol7Collapse.txt
create mode 100644 test/merge/bamCol8Mean.txt
create mode 100644 test/merge/bamCol9Mean.txt
create mode 100644 test/merge/fullFields.bam
create mode 100644 test/merge/mergeBugTest.bed
create mode 100644 test/merge/mixedStrands.bed
create mode 100644 test/merge/precisionTest.bed
create mode 100644 test/merge/testA.vcf
create mode 100644 test/merge/unsorted.bed
create mode 100644 test/shuffle/excl.bed
create mode 100644 test/shuffle/incl.bed
create mode 100644 test/shuffle/simrep.bed
create mode 100644 test/shuffle/test-shuffle.sh
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