[med-svn] [bedtools] branch master updated (c8bfb02 -> a3fefa2)

[Charles Plessy]

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plessy pushed a change to branch master
in repository bedtools.

      from  c8bfb02   Update README.md
       new  77c1bda   Created new KeyListOps class to replace vectorOps. Converted map tool to this.
       new  4793c98   Merge pull request #39 from nkindlon/master
       new  2268ee4   Refactored KeyListOps, Context, mapFile for KeyListOps re-usability by other tools.
       new  8bba882   forgot main Makefile update.
       new  af1113e   More unit tests, also fixed files messed up by previous merge attempt.
       new  1a0737d   Merge pull request #41 from nkindlon/master
       new  a70cc30   added: mm10 mouse genome
       new  8be6539   Merge pull request #40 from theoryno3/master
       new  9509809   Fixed intersect bug so that bed query with Bam DB correctly gives bed output. Added unit test.
       new  733c84b   Merge pull request #43 from nkindlon/master
       new  5032438   [DOC] multiple ops/cols allowed in a single map run. also, speed comparo.
       new  3719038   Setting Release-Version v2.19.1
       new  732f683   Setting Release-Version v2.19.1
       new  a3fefa2   Setting Release-Version v2.19.1

The 14 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 +
 .../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/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/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 +++++++--
 53 files changed, 1567 insertions(+), 432 deletions(-)
 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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