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commit 6b2664688012cc1927bfc4d4d536e92a08edd769 Merge: 8e86672 7b7c16b Author: Andreas Tille <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bowtie2.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
