This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository diamond-aligner.
commit 75907dcc63a86b69d28fc081c97550df66921323 Merge: f798f44 982daa6 Author: Andreas Tille <ti...@debian.org> Date: Wed Jan 25 21:19:35 2017 +0100 Merge tag 'upstream/0.8.34+dfsg' Upstream version 0.8.34+dfsg CMakeLists.txt | 1 + README.rst | 4 +- build_simple.sh | 1 + diamond_manual.pdf | Bin 92606 -> 0 bytes src/ChangeLog | 11 ++ src/align/align.cpp | 14 +- src/align/query_mapper.cpp | 16 +- src/basic/basic.cpp | 2 +- src/basic/config.cpp | 33 +++- src/basic/config.h | 9 +- src/basic/const.h | 2 +- src/basic/hssp.cpp | 2 + src/basic/reduction.h | 1 + src/basic/shape.h | 55 ++++++- src/basic/statistics.h | 5 +- src/basic/value.h | 7 + src/data/frequent_seeds.h | 2 +- src/data/load_seqs.h | 16 +- src/data/reference.h | 10 +- src/data/string_set.h | 7 + src/dp/dp.h | 1 + src/dp/dp_matrix.h | 2 + src/dp/floating_sw.cpp | 6 +- src/dp/growing_buffer.h | 1 + src/dp/padded_banded_sw.cpp | 2 + src/{basic/const.h => extra/extra.h} | 33 +--- src/extra/model_sim.cpp | 11 +- src/extra/opt.cpp | 307 +++++++++++++++++++++++++++++++++++ src/output/daa_file.h | 1 + src/output/join_blocks.cpp | 25 ++- src/output/output.h | 11 +- src/run/benchmark.cpp | 62 +++++-- src/run/double_indexed.cpp | 11 +- src/run/main.cpp | 4 + src/search/align_range.h | 66 ++++++++ src/search/search.cpp | 3 - src/search/setup.cpp | 7 +- src/search/sse_dist.h | 133 --------------- src/search/stage2.cpp | 43 ++++- src/search/trace_pt_buffer.h | 7 +- src/util/async_buffer.h | 68 ++++---- src/util/binary_file.h | 3 +- src/util/double_buffer.h | 1 + src/util/log_stream.h | 20 ++- src/util/system.h | 28 ++++ src/util/tinythread.cpp | 2 + src/util/util.cpp | 1 + src/util/util.h | 14 +- 48 files changed, 772 insertions(+), 299 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/diamond-aligner.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit