This is an automated email from the git hooks/post-receive script. tille pushed a change to branch master in repository diamond-aligner.
from d2d3a75 New upstream version new baec593 New upstream version 0.9.10+dfsg new c5e9593 Updated version 0.9.10+dfsg from 'upstream/0.9.10+dfsg' new aa9a12b New upstream version new c87ab56 Force the symbol with c++ explicit function template instantiation for the latter prototype instead of relying on implicit instantiation Upload and see, whether this will help to fix bug #865132 new 2c10a77 Standards-Version: 4.1.0 (no changes needed) new 608f5e6 Do not parse d/changelog new eaa0274 Fix typo in d/rules and upload to unstable The 7 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 + debian/changelog | 10 + debian/control | 2 +- debian/patches/avoid_unwanted_optimisation.patch | 17 ++ debian/patches/series | 1 + debian/rules | 14 +- 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 ++--- 48 files changed, 861 insertions(+), 591 deletions(-) create mode 100644 debian/patches/avoid_unwanted_optimisation.patch 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