[med-svn] [bowtie2] branch master updated (a142bd4 -> a0c840a)
Andreas Tille
tille at debian.org
Mon Jan 9 12:30:41 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository bowtie2.
from a142bd4 Add EDAM version
new 8e86672 Code available on Github
new 7b7c16b New upstream version 2.3.0
new 6b26646 Merge tag 'upstream/2.3.0'
new 47227a2 New upstream version
new 0115289 debhelper 10
new d7797c3 Remove Carlos Borroto from Uploaders
new 1ec3793 Refresh patches
new 285af78 Drop get-orig-source target which became redundant due to Github download
new 3e76366 --parallel is redundant when using debhelper 10
new a0c840a try to get building including runtime testing but failed
The 10 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 | 26 +
.travis.yml | 20 +
MANUAL | 25 +-
MANUAL.markdown | 26 +-
Makefile | 87 +-
NEWS | 23 +-
README | 8 +
VERSION | 2 +-
aligner_result.cpp | 2 +-
aligner_result.h | 2 +-
aligner_seed.cpp | 16 +-
aligner_seed2.cpp | 19 +-
aligner_seed2.h | 2 -
aligner_sw_common.h | 13 +-
aligner_swsse_ee_i16.cpp | 1 -
aligner_swsse_ee_u8.cpp | 1 -
aligner_swsse_loc_u8.cpp | 1 -
aln_sink.h | 8 -
alphabet.cpp | 199 -
alphabet.h | 72 -
bt2_build.cpp | 14 +-
bt2_inspect.cpp | 6 +-
bt2_search.cpp | 207 +-
cpu_numa_info.cpp | 9 +
cpu_numa_info.h | 6 +
debian/changelog | 12 +
debian/compat | 2 +-
debian/control | 8 +-
debian/copyright | 4 +-
debian/patches/hardening.patch | 32 +-
debian/patches/reproducible.patch | 16 +-
debian/patches/series | 1 +
...st_requiring_non-free_libmath-random-perl.patch | 193 +
debian/rules | 6 +-
debian/watch | 5 +-
diff_sample.h | 2 +-
doc/images/bowtie_logo.png | Bin 0 -> 16419 bytes
doc/images/osi-certified.gif | Bin 0 -> 2712 bytes
doc/images/sflogo.png | Bin 0 -> 1177 bytes
doc/images/university.small.horizontal.white.png | Bin 0 -> 35224 bytes
doc/manual.html | 1417 +++---
doc/release.txt | 153 +
doc/website/faq.shtml | 34 +
doc/website/faq.ssi | 68 +
doc/website/foot.ssi | 12 +
doc/website/index.html | 9 +
doc/website/index.shtml | 60 +
doc/website/manual.shtml | 33 +
doc/{manual.html => website/manual.ssi} | 36 +-
doc/website/news.shtml | 35 +
doc/website/old_news.ssi | 359 ++
doc/website/other_tools.shtml | 33 +
doc/website/push.sh | 17 +
doc/website/push_images.sh | 16 +
doc/website/recent_news.ssi | 104 +
doc/website/rhsidebar.ssi | 196 +
doc/website/top.ssi | 16 +
dp_framer.cpp | 3 +-
dp_framer.h | 3 +-
filebuf.h | 1 +
opts.h | 2 +-
pat.cpp | 2030 ++++----
pat.h | 1852 +++----
pthreadGC2.dll | Bin 0 -> 60273 bytes
read.h | 102 +-
read_qseq.cpp | 383 +-
ref_read.cpp | 34 +-
sam.cpp | 120 +-
sam.h | 8 -
scoring.cpp | 1 -
scoring.h | 2 +-
scripts/sa.py | 79 +
scripts/sim/AlignmentCheck.pm | 859 ++++
scripts/sim/DNA.pm | 287 ++
scripts/sim/Mutate.pm | 301 ++
scripts/sim/RandDNA.pm | 191 +
scripts/sim/SampleRead.pm | 244 +
scripts/sim/Sim.pm | 1040 ++++
scripts/sim/Test.pm | 47 +
scripts/sim/contrib/ForkManager.pm | 412 ++
scripts/sim/run.pl | 133 +
scripts/sim/run.sh | 37 +
scripts/sim/unit.sh | 23 +
scripts/test/.gitignore | 1 +
scripts/test/DNA.pm | 127 +
scripts/test/README.md | 44 +
scripts/test/benchmark/benchmarks.py | 275 ++
scripts/test/benchmark/data/conf/acc.json | 44 +
scripts/test/benchmark/data/conf/seta.bench | 59 +
scripts/test/benchmark/data/conf/speed.json | 44 +
scripts/test/benchmark/run.py | 128 +
scripts/test/benchmark/samreader.py | 128 +
scripts/test/big_data/reads/human_reads.fa | 8 +
scripts/test/big_data/reads/mouse_reads.fa | 8 +
scripts/test/bt2face.py | 39 +
scripts/test/btdata.py | 199 +
scripts/test/dataface.py | 81 +
scripts/test/large_idx.py | 110 +
scripts/test/regressions.py | 207 +
scripts/test/simple_tests.pl | 5070 ++++++++++++++++++++
scripts/test/simple_tests.sh | 34 +
search_globals.h | 5 -
simple_func.h | 4 +
sstring.cpp | 4 +-
sstring.h | 142 +-
threading.h | 46 +-
106 files changed, 14669 insertions(+), 4006 deletions(-)
create mode 100644 .gitignore
create mode 100644 .travis.yml
create mode 100644 README
create mode 100644 cpu_numa_info.cpp
create mode 100644 cpu_numa_info.h
create mode 100644 debian/patches/skip_test_requiring_non-free_libmath-random-perl.patch
create mode 100644 doc/images/bowtie_logo.png
create mode 100644 doc/images/osi-certified.gif
create mode 100644 doc/images/sflogo.png
create mode 100644 doc/images/university.small.horizontal.white.png
create mode 100644 doc/release.txt
create mode 100644 doc/website/faq.shtml
create mode 100644 doc/website/faq.ssi
create mode 100644 doc/website/foot.ssi
create mode 100644 doc/website/index.html
create mode 100644 doc/website/index.shtml
create mode 100644 doc/website/manual.shtml
copy doc/{manual.html => website/manual.ssi} (97%)
create mode 100644 doc/website/news.shtml
create mode 100644 doc/website/old_news.ssi
create mode 100644 doc/website/other_tools.shtml
create mode 100644 doc/website/push.sh
create mode 100644 doc/website/push_images.sh
create mode 100644 doc/website/recent_news.ssi
create mode 100644 doc/website/rhsidebar.ssi
create mode 100644 doc/website/top.ssi
create mode 100644 pthreadGC2.dll
create mode 100644 scripts/sa.py
create mode 100644 scripts/sim/AlignmentCheck.pm
create mode 100644 scripts/sim/DNA.pm
create mode 100644 scripts/sim/Mutate.pm
create mode 100644 scripts/sim/RandDNA.pm
create mode 100644 scripts/sim/SampleRead.pm
create mode 100644 scripts/sim/Sim.pm
create mode 100644 scripts/sim/Test.pm
create mode 100644 scripts/sim/contrib/ForkManager.pm
create mode 100644 scripts/sim/run.pl
create mode 100644 scripts/sim/run.sh
create mode 100644 scripts/sim/unit.sh
create mode 100644 scripts/test/.gitignore
create mode 100644 scripts/test/DNA.pm
create mode 100644 scripts/test/README.md
create mode 100755 scripts/test/benchmark/benchmarks.py
create mode 100644 scripts/test/benchmark/data/conf/acc.json
create mode 100644 scripts/test/benchmark/data/conf/seta.bench
create mode 100644 scripts/test/benchmark/data/conf/speed.json
create mode 100755 scripts/test/benchmark/run.py
create mode 100755 scripts/test/benchmark/samreader.py
create mode 100644 scripts/test/big_data/reads/human_reads.fa
create mode 100644 scripts/test/big_data/reads/mouse_reads.fa
create mode 100755 scripts/test/bt2face.py
create mode 100755 scripts/test/btdata.py
create mode 100755 scripts/test/dataface.py
create mode 100755 scripts/test/large_idx.py
create mode 100755 scripts/test/regressions.py
create mode 100644 scripts/test/simple_tests.pl
create mode 100644 scripts/test/simple_tests.sh
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