[med-svn] [last-align] 06/08: Merge tag 'upstream/731'

[Andreas Tille]

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

commit 6466b6b3b08d82fa3315d1fad1ab836321e0bfb9
Merge: 536af38 e2f7df7
Author: Andreas Tille <tille at debian.org>
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(-)

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