[med-svn] [last-align] branch master updated (83e4a81 -> d98829f)

[Andreas Tille]

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

      from  83e4a81   Upload to unstable
       new  f7e2ac8   Repository is not defined as dictionary
       new  23782ff   Use proper e-mail instead of spam pseudo-protected address
       new  6b2a906   Remove Watch field
       new  536af38   Use xz compression in watch opts
       new  e2f7df7   Imported Upstream version 731
       new  6466b6b   Merge tag 'upstream/731'
       new  97bae00   cme fix dpkg-control
       new  d98829f   Upload to unstable

The 8 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 +-
 debian/changelog                       |     9 +
 debian/control                         |     4 +-
 debian/rules                           |     4 -
 debian/upstream/metadata               |     7 +-
 debian/watch                           |     3 +-
 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 +-
 71 files changed, 37003 insertions(+), 36468 deletions(-)
 create mode 100644 src/SubsetMinimizerFinder.cc
 create mode 100644 src/SubsetMinimizerFinder.hh
 create mode 100644 src/threadUtil.hh

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/last-align.git