[med-svn] [seer] branch master updated (dd0c779 -> d43289c)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository seer.

      from  dd0c779   Upload to unstable
       new  e36dd9b   New upstream version 1.1.4
       new  2cdaa87   Merge tag 'upstream/1.1.4'
       new  a9f126a   New upstream version
       new  b06d116   Standards-Version: 4.1.0 (no changes needed)
       new  2304a54   Update patches
       new  b0ad529   New upstream version 1.1.4
       new  6e67d7f   Merge tag 'upstream/1.1.4'
       new  d43289c   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:
 .gitignore                               |   1 -
 .gitmodules                              |   3 +
 .travis.yml                              |   6 +-
 README.md                                |  24 ++-
 debian/changelog                         |   7 +
 debian/control                           |   2 +-
 debian/patches/fix_lib_location.patch    |   2 +-
 debian/patches/hardening.patch           |   2 +-
 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 +++++++++++++-------------
 45 files changed, 1582 insertions(+), 1230 deletions(-)
 create mode 100755 scripts/blastn_to_phandango.pl
 create mode 100644 src/seerBasicFilter.cpp
 delete mode 100644 src/seerFilter.cpp
 rename src/{seerChiFilter.cpp => seerStats.cpp} (58%)

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