[med-svn] [bedops] 02/03: Updated version 2.4.28+dfsg from 'upstream/2.4.28+dfsg'
Steffen Möller
moeller at moszumanska.debian.org
Fri Oct 20 21:58:31 UTC 2017
This is an automated email from the git hooks/post-receive script.
moeller pushed a commit to branch master
in repository bedops.
commit 7921366f4fe4bbaaeb053f6914b12dc9ee40c518
Merge: ecdfa9b 2763b0f
Author: Steffen Moeller <moeller at debian.org>
Date: Mon Sep 11 14:23:45 2017 +0200
Updated version 2.4.28+dfsg from 'upstream/2.4.28+dfsg'
with Debian dir aa1bf20a5ce3654711e441eede21f4d1a0cb08f1
.gitignore | 8 +
.travis.yml | 4 +-
Makefile | 368 +++-
README.md | 19 +-
applications/bed/bedextract/src/ExtractRows.cpp | 51 +-
applications/bed/bedextract/src/Makefile | 24 +-
applications/bed/bedextract/src/Makefile.darwin | 28 +-
applications/bed/bedmap/doc/known.issues | 33 -
applications/bed/bedmap/src/Bedmap.cpp | 465 +++--
applications/bed/bedmap/src/Input.hpp | 6 +-
applications/bed/bedmap/src/Makefile | 21 +-
applications/bed/bedmap/src/Makefile.darwin | 27 +-
applications/bed/bedmap/src/TDefs.hpp | 2 +-
.../bed/bedops/doc/Usage.Statement.Version1.2 | 35 -
applications/bed/bedops/src/BedPadReader.hpp | 18 +-
applications/bed/bedops/src/Bedops.cpp | 315 ++--
applications/bed/bedops/src/Makefile | 21 +-
applications/bed/bedops/src/Makefile.darwin | 29 +-
applications/bed/closestfeats/src/BedReader.hpp | 17 +-
.../bed/closestfeats/src/ClosestFeature.cpp | 89 +-
applications/bed/closestfeats/src/Makefile | 21 +-
applications/bed/closestfeats/src/Makefile.darwin | 29 +-
applications/bed/conversion/src/Makefile | 42 +-
applications/bed/conversion/src/Makefile.darwin | 32 +-
applications/bed/conversion/src/convert2bed.c | 1812 ++++++++++++++------
applications/bed/conversion/src/convert2bed.h | 686 ++++----
.../bed/conversion/src/tests/bam/split2.bam | Bin 0 -> 1388 bytes
.../bed/conversion/src/tests/bam/split2.sam | 29 +
applications/bed/conversion/src/wrappers/bam2bed | 18 +-
.../bed/conversion/src/wrappers/bam2starch | 18 +-
applications/bed/conversion/src/wrappers/sam2bed | 18 +-
.../bed/conversion/src/wrappers/sam2starch | 18 +-
applications/bed/sort-bed/src/CheckSort.cpp | 10 +-
applications/bed/sort-bed/src/Makefile | 68 +-
applications/bed/sort-bed/src/Makefile.darwin | 101 +-
applications/bed/sort-bed/src/Sort.cpp | 33 +-
applications/bed/sort-bed/src/SortDetails.cpp | 8 +-
applications/bed/sort-bed/src/Structures.hpp | 3 -
.../src/update-sort-bed-migrate-candidates.py | 2 +-
.../bed/sort-bed/src/update-sort-bed-slurm.py | 2 +-
.../sort-bed/src/update-sort-bed-starch-slurm.py | 4 +-
applications/bed/starch/src/Makefile | 70 +-
applications/bed/starch/src/Makefile.darwin | 93 +-
applications/bed/starch/src/starch-diff.py | 11 +-
applications/bed/starch/src/starch.c | 40 +-
applications/bed/starch/src/starch.h | 10 +
applications/bed/starch/src/starchcat.c | 704 +++++---
applications/bed/starch/src/starchcat.h | 13 +
.../bed/starch/src/starchcluster_gnuParallel.tcsh | 2 +-
applications/bed/starch/src/starchcluster_sge.tcsh | 2 +-
.../bed/starch/src/starchcluster_slurm.tcsh | 2 +-
applications/bed/starch/src/starchstrip.c | 184 +-
applications/bed/starch/src/starchstrip.h | 10 +
applications/bed/starch/src/unstarch.c | 364 ++--
applications/bed/starch/src/unstarch.h | 19 +-
applications/other/switch-BEDOPS-binary-type | 76 +
docs/conf.py | 2 +-
docs/content/installation.rst | 56 +-
.../reference/file-management/compression.rst | 2 +-
.../file-management/compression/starch-diff.rst | 2 +-
.../file-management/compression/starch.rst | 2 +-
.../file-management/compression/starchcat.rst | 2 +-
.../file-management/compression/starchstrip.rst | 4 +-
.../file-management/compression/unstarch.rst | 2 +-
.../file-management/conversion/gtf2bed.rst | 12 +-
.../file-management/conversion/psl2bed.rst | 2 +-
.../file-management/conversion/vcf2bed.rst | 2 +-
.../reference/file-management/sorting/sort-bed.rst | 2 +-
.../reference/set-operations/bedextract.rst | 2 +-
docs/content/reference/set-operations/bedops.rst | 2 +-
.../reference/set-operations/closest-features.rst | 2 +-
docs/content/reference/statistics/bedmap.rst | 11 +-
docs/content/release.rst | 20 +-
docs/content/revision-history.rst | 120 +-
docs/content/usage-examples/snps-within-dhses.rst | 2 +-
docs/index.rst | 18 +-
.../general-headers/algorithm/bed/FindBedRange.hpp | 59 +-
.../algorithm/visitors/Visitors.hpp | 4 +-
.../algorithm/visitors/bed/BedBaseVisitor.hpp | 8 +-
.../visitors/helpers/ProcessBedVisitorRow.hpp | 21 +-
.../visitors/numerical/ExtremeVisitor.hpp | 2 +-
.../algorithm/visitors/other/MultiVisitor.hpp | 12 +-
.../data/bed/AllocateIterator_BED_starch.hpp | 73 +-
....hpp => AllocateIterator_BED_starch_minmem.hpp} | 42 +-
interfaces/general-headers/data/bed/Bed.hpp | 556 +++---
.../general-headers/data/bed/BedCheckIterator.hpp | 134 +-
...eckIterator.hpp => BedCheckIterator_minmem.hpp} | 60 +-
interfaces/general-headers/data/bed/BedCompare.hpp | 109 +-
interfaces/general-headers/data/bed/BedTypes.hpp | 39 +-
interfaces/general-headers/data/bed/Bed_minmem.hpp | 917 ++++++++++
.../general-headers/data/starch/starchApi.hpp | 38 +-
.../general-headers/data/starch/starchHelpers.h | 4 +-
.../general-headers/suite/BEDOPS.Constants.hpp | 51 +-
.../general-headers/suite/BEDOPS.Version.hpp | 4 +-
.../utility/{PooledMemory.hpp => BitMonitor.hpp} | 381 ++--
.../general-headers/utility/CharPooledMemory.hpp | 521 ++++++
.../{SingletonType.hpp => CompilerMath.hpp} | 41 +-
.../general-headers/utility/PooledMemory.hpp | 365 +---
interfaces/general-headers/utility/PrintTypes.hpp | 24 +-
.../general-headers/utility/SingletonType.hpp | 18 +-
interfaces/general-headers/utility/Typify.hpp | 24 +-
interfaces/src/algorithm/sweep/WindowSweepImpl.cpp | 79 +-
.../algorithm/sweep/WindowSweepImpl.specialize.cpp | 24 +-
interfaces/src/data/starch/starchHelpers.c | 177 +-
interfaces/src/data/starch/starchMetadataHelpers.c | 17 +-
interfaces/src/data/starch/starchSha1Digest.c | 342 ++--
interfaces/src/data/starch/unstarchHelpers.c | 52 +-
interfaces/src/utility/SingletonType.cpp | 14 +
packaging/deb/Dockerfile | 8 +-
packaging/deb/control | 2 +-
packaging/os_x/BEDOPS.pkgproj | 1197 ++++++++++++-
packaging/rpm/Dockerfile | 12 +-
packaging/rpm/bedops.spec | 2 +-
system.mk/Makefile.darwin | 303 +---
system.mk/Makefile.linux | 149 +-
115 files changed, 8235 insertions(+), 4051 deletions(-)
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