[med-svn] [bedtools] branch master updated (7c29e82 -> 4122ba1)
Charles Plessy
plessy at moszumanska.debian.org
Sat May 24 13:25:33 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 7c29e82 [DOC] add new usage examples from the wild
new e7f41f5 [DOC] add new usage examples from the wild
new 9e50ca3 tweak README
new 377f1b1 remove extraneous header tab
new ed71c8e fix most filetype issues. intersect still raises error with empty files.
new 4642a14 [ENH] all shuffle with -incl to follow data distribution
new bcbd75b [TST] run shuffle tests.
new f36d6db Merge converted to PFM, first check-in
new 8b6ed4b Merge branch 'master' of https://github.com/nkindlon/bedtools2
new fe5ea0e Handling empty files with headers
new eb2f614 Merge remote-tracking branch 'upstream/master' into merge
new 8284c92 Fixed merge conflicts
new 5eb3b68 Unit tests and bug fixes for merge release
new 9eb4337 Merge branch 'merge'
new 1b866b6 Final unit tests for merge, including stranded merge bug fixes.
new 3b04625 Merge branch 'merge'
new fccfbfb Merge pull request #53 from nkindlon/master
new d0fe42c allow merge -d to have negative values for minimum overlap.
new 4fd41ae add missing help menu items (-S -header) to merge
new c5d1e72 cleanup KeyListOps help formatting
new 17ec9aa cleanup unit tests.
new 57ce8d4 allow command line includes for make
new fd7becf support for operators 'X' and '=' in method BlockedIntervals.cpp/GetBamBlocks
new ba984f3 Merge pull request #63 from lindenb/fixBlockedIntervals
new 70345fd Update BlockMgr.cpp
new 4ef1d94 Test commit
new b740bbf merge bug fixes and unit tests
new bbda1f4 Made Merge only print Bed3 output for BAM, added unit test
new e2be078 Added jaccard w/ -split and unit tests. Fixed Bam input as bam output bug, added unit test in sample.
new 39fffc9 Added stranded info to jaccard and merge help, fixed stranded jaccard bug
new e866785 added changes to stop CLANG compiler warnings.
new be32e1c Added unit test to merge to confirm precision
new 952140c Changes fetch columns by number from BAM files.
new d42edc9 Merge pull request #64 from nkindlon/master
new 77fae72 Merge pull request #67 from nkindlon/master
new 3f03f6d [DOC] fix formatting for unionbedg
new aece1e8 [DOC] fix formatting for unionbedg
new 656fd84 Merge pull request #68 from nkindlon/master
new 0b41d1a Merge pull request #69 from nkindlon/master
new 143be5d Update installation.rst
new 502c94d Merge pull request #75 from alexpenson/patch-1
new 9ee6bac Allowed numeric ops for non-numeric columns
new 47a801b Updated map's unit test for allowance of numeric ops on non-num cols
new 2ae5c07 Stripped whitespace and DOS endLine chars in parsing.
new d358798 Fixed map and merge help messages.
new 44c8771 Merge pull request #76 from nkindlon/master
new 9e886b4 Resolved merge conflicts with KeyListOps.cpp, test-merge.sh, and test-map.sh
new bc90a1a More unit tests for column ops on BAM
new f7fc153 Merge pull request #79 from nkindlon/master
new 69eb4ea correct intersect unit test - was pointing to test binary
new 47c6a2e tweaks for 2.20.0
new 0cd7017 Setting Release-Version v2.20.0
new 364f619 docs formatting
new 4a5fc54 fix for slop bug in issue \#82
new 18eb97a updates for 2.20.1
new d8c6201 Fixed bug for files with no newlines.
new 2c9675e Merge pull request #83 from nkindlon/master
new fa9ab3b update history for 2.20.1
new 4122ba1 Setting Release-Version v2.20.1
The 58 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 +
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 +
137 files changed, 5903 insertions(+), 2148 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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