[med-svn] [seer] branch upstream updated (df7df2f -> b0ad529)

[Andreas Tille]

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

tille pushed a change to branch upstream
in repository seer.

      from  df7df2f   New upstream version 1.1.2
       new  b0ad529   New upstream version 1.1.4

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:
 .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(-)
 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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