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commit 6466b6b3b08d82fa3315d1fad1ab836321e0bfb9 Merge: 536af38 e2f7df7 Author: Andreas Tille <[email protected]> Date: Sat Mar 12 07:57:47 2016 +0100 Merge tag 'upstream/731' Upstream version 731 ChangeLog.txt | 109 +- doc/bisulfite.html | 12 +- doc/bisulfite.txt | 13 +- doc/last-tuning.html | 76 +- doc/last-tuning.txt | 63 +- doc/last.html | 23 +- doc/last.txt | 22 +- doc/lastal.html | 30 +- doc/lastal.txt | 31 +- doc/lastdb.html | 18 + doc/lastdb.txt | 20 + makefile | 2 +- scripts/maf-convert | 95 +- src/Alignment.hh | 15 +- src/AlignmentWrite.cc | 25 +- src/CyclicSubsetSeed.cc | 2 +- src/CyclicSubsetSeed.hh | 21 + src/LastalArguments.cc | 25 +- src/LastalArguments.hh | 3 + src/LastdbArguments.cc | 21 +- src/LastdbArguments.hh | 3 + src/Mmap.hh | 14 +- src/MultiSequence.cc | 2 +- src/MultiSequence.hh | 23 +- src/MultiSequenceQual.cc | 10 +- src/SubsetMinimizerFinder.cc | 49 + src/SubsetMinimizerFinder.hh | 52 + src/SubsetSuffixArray.cc | 31 +- src/SubsetSuffixArray.hh | 8 +- src/SubsetSuffixArraySort.cc | 19 +- src/VectorOrMmap.hh | 4 +- src/alp/njn_dynprogprob.cpp | 590 +- src/alp/njn_ioutil.cpp | 334 +- src/alp/njn_localmaxstat.hpp | 396 +- src/alp/njn_random.cpp | 204 +- src/alp/njn_random.hpp | 110 +- src/alp/njn_uniform.hpp | 152 +- src/alp/sls_alignment_evaluer.cpp | 2300 +-- src/alp/sls_alignment_evaluer.hpp | 420 +- src/alp/sls_alp.cpp | 4732 +++---- src/alp/sls_alp.hpp | 728 +- src/alp/sls_alp_data.cpp | 3326 ++--- src/alp/sls_alp_data.hpp | 1874 +-- src/alp/sls_alp_sim.cpp | 9098 ++++++------ src/alp/sls_alp_sim.hpp | 1158 +- src/alp/sls_basic.cpp | 344 +- src/alp/sls_basic.hpp | 424 +- src/alp/sls_falp_alignment_evaluer.cpp | 2140 +-- src/alp/sls_falp_alignment_evaluer.hpp | 374 +- src/alp/sls_fsa1.cpp | 23178 +++++++++++++++---------------- src/alp/sls_fsa1.hpp | 2832 ++-- src/alp/sls_fsa1_parameters.cpp | 3624 ++--- src/alp/sls_fsa1_parameters.hpp | 452 +- src/alp/sls_fsa1_pvalues.cpp | 2696 ++-- src/alp/sls_fsa1_pvalues.hpp | 686 +- src/alp/sls_fsa1_utils.cpp | 4400 +++--- src/alp/sls_fsa1_utils.hpp | 2274 +-- src/alp/sls_pvalues.cpp | 2694 ++-- src/alp/sls_pvalues.hpp | 652 +- src/fileMap.cc | 8 +- src/fileMap.hh | 6 +- src/lastal.cc | 155 +- src/lastdb.cc | 162 +- src/makefile | 40 +- src/threadUtil.hh | 38 + src/version.hh | 2 +- 66 files changed, 36988 insertions(+), 36456 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/last-align.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
