This is an automated email from the git hooks/post-receive script. tille pushed a change to branch upstream in repository diamond-aligner.
from e37193d New upstream version 0.9.8+dfsg new baec593 New upstream version 0.9.10+dfsg The 1 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: CMakeLists.txt | 4 + README.rst | 2 +- build_simple.sh | 4 + src/ChangeLog | 14 +- src/align/align.cpp | 288 ++++----------------- src/align/align.h | 64 +---- src/align/align_queries.h | 67 ----- src/align/align_target.cpp | 4 + src/align/query_mapper.cpp | 133 +++++----- src/align/query_mapper.h | 16 ++ src/basic/basic.cpp | 4 +- src/basic/config.cpp | 28 +- src/basic/config.h | 6 +- src/basic/const.h | 2 +- src/basic/hssp.cpp | 30 ++- src/basic/match.h | 2 + src/basic/sequence.h | 9 +- src/basic/value.h | 2 +- src/data/load_seqs.h | 12 +- src/data/reference.cpp | 22 ++ src/data/reference.h | 9 +- src/data/taxonomy.cpp | 81 +++++- src/data/taxonomy.h | 15 ++ src/dp/dp.h | 7 +- src/dp/swipe.cpp | 2 +- src/extra/match_file.h | 1 + src/output/blast_pairwise_format.cpp | 5 +- src/output/blast_tab_format.cpp | 8 +- src/output/join_blocks.cpp | 51 +++- src/output/output.h | 39 ++- src/output/output_format.cpp | 25 +- src/output/output_format.h | 69 ++++- src/output/output_sink.cpp | 86 ++++++ src/output/sam_format.cpp | 2 +- src/{util/system_c.h => output/target_culling.cpp} | 14 +- src/output/target_culling.h | 73 ++++++ src/output/taxon_format.cpp | 51 ++++ src/output/{view.h => view.cpp} | 67 ++--- src/run/double_indexed.cpp | 10 +- src/run/main.cpp | 7 +- src/run/tools.cpp | 6 +- src/util/log_stream.h | 5 + src/util/{high_res_timer.h => queue.h} | 62 ++--- 43 files changed, 825 insertions(+), 583 deletions(-) delete mode 100644 src/align/align_queries.h create mode 100644 src/output/output_sink.cpp copy src/{util/system_c.h => output/target_culling.cpp} (80%) create mode 100644 src/output/target_culling.h create mode 100644 src/output/taxon_format.cpp rename src/output/{view.h => view.cpp} (73%) copy src/util/{high_res_timer.h => queue.h} (62%) -- 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