[med-svn] [salmon] branch master updated (393bd0a -> 83ec434)
Andreas Tille
tille at debian.org
Tue Jan 24 13:17:28 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository salmon.
from 393bd0a update d/changelog
new 993416c New upstream version 0.8.0+ds1
new ab1af01 Merge tag 'upstream/0.8.0+ds1'
new a87ef14 Try hard to adapt all patches
new 8251ca6 New upstream version
new bedfbe0 debhelper 10
new 0ff42d1 d/watch: version=4
new 83ec434 Does not build - add TODO item to changelog
The 7 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:
.drone.yml | 26 +
.drone.yml.sig | 1 +
.drone/build.sh | 19 +
.drone/copy_build.sh | 10 +
.drone/test_quant.sh | 27 +
CMakeLists.txt | 162 +-
debian/changelog | 14 +
debian/compat | 2 +-
debian/control | 2 +-
...007-Remove-unnecessarily-linked-libraries.patch | 39 +-
debian/patches/0008-Remove-salmon_core-lib.patch | 18 +-
...emove-FIND_PACKAGE-for-liblzma-and-libbz2.patch | 68 +-
debian/patches/add_MEM_F_SELF_OVLP.patch | 4 +-
debian/patches/cmake-typo-fixes | 2 +-
debian/patches/dependency-fix | 412 +--
debian/patches/disable-version-check | 6 +-
debian/patches/fix-unittest.patch | 2 +-
debian/patches/reproducible.patch | 6 +-
debian/patches/use-system-pkg-config-tbb | 16 +-
debian/patches/use_debian_packaged_rapmap.patch | 23 +-
debian/rules | 2 +
debian/watch | 6 +-
doc/source/salmon.rst | 8 +-
include/AlignmentLibrary.hpp | 96 +
include/CollapsedGibbsSampler.hpp | 11 +-
include/EquivalenceClassBuilder.hpp | 2 +-
include/FragmentLengthDistribution.hpp | 11 +-
include/GCFragModel.hpp | 334 +-
include/GZipWriter.hpp | 7 +-
include/PartitionRefiner.hpp | 42 -
include/PerfectHashIndex.hpp | 174 -
include/ReadExperiment.hpp | 132 +-
include/ReadPair.hpp | 7 +-
include/SailfishUtils.hpp | 153 -
include/SalmonConfig.hpp | 9 +-
include/SalmonIndex.hpp | 9 +-
include/SalmonOpts.hpp | 29 +-
include/SalmonUtils.hpp | 6 +-
include/Sampler.hpp | 86 +-
include/SimplePosBias.hpp | 6 +
include/Transcript.hpp | 101 +-
include/TranscriptGeneMap.hpp | 16 +-
include/UnpairedRead.hpp | 2 +-
include/btree.h | 2394 -------------
include/btree_container.h | 350 --
include/btree_map.h | 130 -
include/btree_set.h | 121 -
include/concurrentqueue.h | 4 +-
include/count_main_cmdline.hpp | 711 ----
include/cuckoohash_config.hh | 14 +-
include/cuckoohash_map.hh | 3572 +++++++++++---------
include/cuckoohash_util.hh | 81 +-
include/lazy_array.hh | 119 -
include/libcuckoo_lazy_array.hh | 202 ++
include/merge_files.hpp | 30 -
include/pcg_extras.hpp | 638 ++++
include/pcg_random.hpp | 1756 ++++++++++
include/safe_btree.h | 395 ---
include/safe_btree_map.h | 89 -
include/safe_btree_set.h | 88 -
scripts/ConvertBootstrapsToTSV.py | 9 +-
scripts/Dockerfile | 34 +
scripts/fetchRapMap.sh | 4 +-
scripts/make-release.sh | 3 +
scripts/test_sim_corr.py | 48 +
src/BuildSalmonIndex.cpp | 14 +-
src/CMakeLists.txt | 40 +-
src/CollapsedEMOptimizer.cpp | 227 +-
src/CollapsedGibbsSampler.cpp | 774 ++++-
src/FASTAParser.cpp | 38 +-
src/FragmentLengthDistribution.cpp | 51 +-
src/GZipWriter.cpp | 158 +-
src/JellyfishMerCounter.cpp | 379 ---
src/LookUpTableUtils.cpp | 255 --
src/SailfishUtils.cpp | 699 ----
src/Salmon.cpp | 123 +-
src/SalmonQuantify.cpp | 382 ++-
src/SalmonQuantifyAlignments.cpp | 213 +-
src/SalmonUtils.cpp | 347 +-
src/SimplePosBias.cpp | 20 +-
tests/test_quant.nf | 71 +
81 files changed, 7709 insertions(+), 8982 deletions(-)
create mode 100644 .drone.yml
create mode 100644 .drone.yml.sig
create mode 100755 .drone/build.sh
create mode 100755 .drone/copy_build.sh
create mode 100755 .drone/test_quant.sh
delete mode 100644 include/PartitionRefiner.hpp
delete mode 100644 include/PerfectHashIndex.hpp
delete mode 100644 include/SailfishUtils.hpp
delete mode 100755 include/btree.h
delete mode 100755 include/btree_container.h
delete mode 100755 include/btree_map.h
delete mode 100755 include/btree_set.h
delete mode 100644 include/count_main_cmdline.hpp
delete mode 100644 include/lazy_array.hh
create mode 100644 include/libcuckoo_lazy_array.hh
delete mode 100644 include/merge_files.hpp
create mode 100644 include/pcg_extras.hpp
create mode 100644 include/pcg_random.hpp
delete mode 100755 include/safe_btree.h
delete mode 100755 include/safe_btree_map.h
delete mode 100755 include/safe_btree_set.h
create mode 100644 scripts/Dockerfile
create mode 100644 scripts/test_sim_corr.py
delete mode 100644 src/JellyfishMerCounter.cpp
delete mode 100644 src/LookUpTableUtils.cpp
delete mode 100644 src/SailfishUtils.cpp
create mode 100644 tests/test_quant.nf
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