[med-svn] [last-align] branch upstream updated (f8ba76d -> e2f7df7)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository last-align.

      from  f8ba76d   Imported Upstream version 712
       new  e2f7df7   Imported Upstream version 731

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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(-)
 create mode 100644 src/SubsetMinimizerFinder.cc
 create mode 100644 src/SubsetMinimizerFinder.hh
 create mode 100644 src/threadUtil.hh

-- 
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