[med-svn] [bowtie2] 03/10: Merge tag 'upstream/2.3.0'
Andreas Tille
tille at debian.org
Mon Jan 9 12:30:42 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bowtie2.
commit 6b2664688012cc1927bfc4d4d536e92a08edd769
Merge: 8e86672 7b7c16b
Author: Andreas Tille <tille at debian.org>
Date: Mon Jan 9 12:53:18 2017 +0100
Merge tag 'upstream/2.3.0'
Upstream version 2.3.0
.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 +
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 +-
96 files changed, 14429 insertions(+), 3967 deletions(-)
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