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tille pushed a commit to branch master
in repository diamond-aligner.
commit c5e9593e49b8ca59317dc3ea11de82ab284f723e
Merge: d2d3a75 baec593
Author: Andreas Tille <ti...@debian.org>
Date: Mon Sep 18 13:30:40 2017 +0200
Updated version 0.9.10+dfsg from 'upstream/0.9.10+dfsg'
with Debian dir d7e6526cc3f25884323dd55b00e1052088978fa5
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/{basic/const.h => output/target_culling.cpp} | 30 +--
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/{basic/const.h => util/queue.h} | 59 +++--
43 files changed, 830 insertions(+), 591 deletions(-)
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