[med-svn] [last-align] 02/04: Merge tag 'upstream/869'

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository last-align.

commit 0e7bcc0635b51679c6390073d790d57b93ceb2aa
Merge: 34b894a 00a898d
Author: Sascha Steinbiss <satta at 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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