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commit 0e7bcc0635b51679c6390073d790d57b93ceb2aa
Merge: 34b894a 00a898d
Author: Sascha Steinbiss <sa...@debian.org>
Date: Fri Aug 11 15:16:57 2017 -0400
Merge tag 'upstream/869'
Upstream version 869
ChangeLog.txt | 198 +++++++++++++-
doc/last-dotplot.html | 126 ++++++++-
doc/last-dotplot.txt | 99 +++++--
doc/last-papers.html | 5 +
doc/last-papers.txt | 8 +
doc/last-train.html | 24 +-
doc/last-train.txt | 21 +-
doc/last-tutorial.html | 28 +-
doc/last-tutorial.txt | 27 +-
doc/lastal.html | 12 +-
doc/lastal.txt | 12 +-
doc/lastdb.html | 2 +-
doc/lastdb.txt | 2 +-
scripts/last-dotplot | 463 ++++++++++++++++++++++++---------
scripts/last-postmask | 8 +-
scripts/last-train | 129 ++++++---
scripts/maf-convert | 52 ++--
src/Alignment.cc | 25 +-
src/AlignmentWrite.cc | 5 +-
src/Centroid.cc | 52 ++--
src/Centroid.hh | 13 +-
src/LastEvaluer.cc | 17 +-
src/LastalArguments.cc | 25 +-
src/LastalArguments.hh | 1 +
src/LastdbArguments.cc | 18 +-
src/alp/sls_alignment_evaluer.cpp | 14 +-
src/alp/sls_alignment_evaluer.hpp | 4 +-
src/alp/sls_alp_data.cpp | 9 +-
src/alp/sls_alp_data.hpp | 4 +
src/alp/sls_basic.hpp | 8 +-
src/alp/sls_falp_alignment_evaluer.cpp | 10 -
src/alp/sls_fsa1_pvalues.cpp | 54 +---
src/alp/sls_fsa1_pvalues.hpp | 21 --
src/alp/sls_pvalues.cpp | 54 +---
src/alp/sls_pvalues.hpp | 20 --
src/getoptUtil.hh | 17 ++
src/lastal.cc | 13 +-
src/makefile | 4 +-
src/split/cbrc_split_aligner.hh | 2 +-
src/split/last-split.cc | 15 +-
src/version.hh | 2 +-
41 files changed, 1113 insertions(+), 510 deletions(-)
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