[med-svn] [bedops] branch master updated (ecdfa9b -> 9d517a3)
Steffen Möller
moeller at moszumanska.debian.org
Fri Oct 20 21:58:30 UTC 2017
This is an automated email from the git hooks/post-receive script.
moeller pushed a change to branch master
in repository bedops.
from ecdfa9b Added references to registries.
new 2763b0f New upstream version 2.4.28+dfsg
new 7921366 Updated version 2.4.28+dfsg from 'upstream/2.4.28+dfsg'
new 9d517a3 upstream/metadata: RRID->SciCrunch
The 3 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:
.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 ++++----
.../src/tests/bam/{split.bam => split2.bam} | Bin 1385 -> 1388 bytes
.../src/tests/{sam/split.sam => bam/split2.sam} | 2 +-
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 +
debian/upstream/metadata | 2 +-
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 ++++++
.../utility/{ByLine.hpp => CompilerMath.hpp} | 48 +-
.../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 +-
116 files changed, 8207 insertions(+), 4061 deletions(-)
delete mode 100644 applications/bed/bedmap/doc/known.issues
delete mode 100644 applications/bed/bedops/doc/Usage.Statement.Version1.2
copy applications/bed/conversion/src/tests/bam/{split.bam => split2.bam} (84%)
copy applications/bed/conversion/src/tests/{sam/split.sam => bam/split2.sam} (92%)
create mode 100755 applications/other/switch-BEDOPS-binary-type
copy interfaces/general-headers/data/bed/{AllocateIterator_BED_starch.hpp => AllocateIterator_BED_starch_minmem.hpp} (85%)
copy interfaces/general-headers/data/bed/{BedCheckIterator.hpp => BedCheckIterator_minmem.hpp} (94%)
create mode 100644 interfaces/general-headers/data/bed/Bed_minmem.hpp
copy interfaces/general-headers/utility/{PooledMemory.hpp => BitMonitor.hpp} (61%)
create mode 100644 interfaces/general-headers/utility/CharPooledMemory.hpp
copy interfaces/general-headers/utility/{ByLine.hpp => CompilerMath.hpp} (53%)
mode change 100755 => 100644
create mode 100644 interfaces/src/utility/SingletonType.cpp
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