[med-svn] [seer] 02/08: Merge tag 'upstream/1.1.4'

[Andreas Tille]

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tille pushed a commit to branch master
in repository seer.

commit 2cdaa878900267e30eeab4551454ce5f50a25b62
Merge: dd0c779 e36dd9b
Author: Andreas Tille <tille at debian.org>
Date:   Thu Sep 28 13:18:08 2017 +0200

    Merge tag 'upstream/1.1.4'
    
    Upstream version 1.1.4

 .gitignore                               |   1 -
 .gitmodules                              |   3 +
 .travis.yml                              |   6 +-
 README.md                                |  24 ++-
 scripts/R_mds.pl                         |  48 ++++-
 scripts/blastn_to_phandango.pl           |  88 ++++++++
 scripts/mapping_to_phandango.pl          |  43 ++--
 src/Makefile                             |   6 +-
 src/filterCmdLine.cpp                    |   2 +-
 src/kmds.hpp                             |   2 +-
 src/kmdsMain.cpp                         |   3 +-
 src/kmer.cpp                             |  16 +-
 src/kmer.hpp                             |   7 +-
 src/linearFunction.cpp                   |   4 +-
 src/logitFunction.cpp                    |  35 +--
 src/seer.hpp                             |  22 +-
 src/seerBasicFilter.cpp                  |  33 +++
 src/seerBinaryAssoc.cpp                  |  42 +++-
 src/seerContinuousAssoc.cpp              |  49 +++--
 src/seerFilter.cpp                       |  79 -------
 src/seerIO.cpp                           |  34 +--
 src/seerMain.cpp                         |  42 ++--
 src/{seerChiFilter.cpp => seerStats.cpp} | 111 +++++++++-
 src/seercommon.hpp                       |  11 +-
 src/significant_kmer.cpp                 |  24 ++-
 src/significant_kmer.hpp                 |   7 +-
 test/filter_in.txt                       | 350 +++++++++++++++---------------
 test/map_in.txt                          |   4 +-
 test/test1.e.txt                         |   5 +-
 test/test1.o.txt                         |   2 +-
 test/test2.e.txt                         |   5 +-
 test/test2.o.txt                         | 350 +++++++++++++++---------------
 test/test3.e.txt                         |   5 +-
 test/test3.o.txt                         | 192 ++++++++---------
 test/test4.e.txt                         |   7 +-
 test/test4.o.txt                         | 113 ++++++++--
 test/test5.e.txt                         |   5 +-
 test/test5.o.txt                         | 358 +++++++++++++++----------------
 test/test6.e.txt                         |   5 +-
 test/test6.o.txt                         | 350 +++++++++++++++---------------
 test/test7.o.txt                         | 306 +++++++++++++-------------
 41 files changed, 1572 insertions(+), 1227 deletions(-)

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