[med-svn] [seer] branch upstream updated (954fcd0 -> df7df2f)

[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  954fcd0   Imported Upstream version 1.1.1
       new  df7df2f   New upstream version 1.1.2

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                          |     3 +-
 .travis.yml                         |    18 +
 README.md                           |    47 +-
 scripts/R_mds.pl                    |   143 +
 scripts/blast_top_hits.pl           |     2 +-
 scripts/mash2matrix.pl              |    60 +
 seer-logo.png                       |   Bin 0 -> 30410 bytes
 src/Makefile                        |     9 +
 src/filterCmdLine.cpp               |     6 +
 src/filter_seer.hpp                 |     3 +
 src/kmdsCmdLine.cpp                 |     8 +-
 src/kmdsStruct.cpp                  |     5 +-
 src/mapCmdLine.cpp                  |     6 +
 src/mapMain.cpp                     |     6 +
 src/map_back.hpp                    |     1 +
 src/seerBinaryAssoc.cpp             |     2 +-
 src/seerCmdLine.cpp                 |     7 +-
 src/seerCommon.cpp                  |     9 -
 src/seerFilter.cpp                  |    31 +-
 src/seerIO.cpp                      |     6 +-
 src/seerMain.cpp                    |     9 +
 src/seercommon.hpp                  |     4 +-
 src/significant_kmer.cpp            |    38 +-
 src/significant_kmer.hpp            |     6 +
 test/6259_5_16.fa                   | 35643 ++++++++++++++++++++++++++++++++++
 test/all_structure_new              |   Bin 75800 -> 196442 bytes
 test/assembly_locations.txt         |     1 +
 test/map_in.txt                     |     2 +
 test/run_test.pl                    |    25 +-
 test/{test1.txt => test1.e.txt}     |     4 +-
 test/test1.o.txt                    |     1 +
 test/{test1.txt => test2.e.txt}     |     4 +-
 test/{test2.txt => test2.o.txt}     |     3 -
 test/{test1.txt => test3.e.txt}     |     4 +-
 test/{test3.txt => test3.o.txt}     |     3 -
 test/test4.e.txt                    |     6 +
 test/{test4.txt => test4.o.txt}     |     3 -
 test/{test1.txt => test5.e.txt}     |     4 +-
 test/{test5.txt => test5.o.txt}     |     3 -
 test/{test1.txt => test6.e.txt}     |     4 +-
 test/{filter_in.txt => test6.o.txt} |     0
 test/test6.txt                      |   178 -
 test/test7.e.txt                    |     2 +
 test/{test7.txt => test7.o.txt}     |   308 +-
 test/test8.e.txt                    |     4 +
 test/test8.o.txt                    |     1 +
 46 files changed, 36221 insertions(+), 411 deletions(-)
 create mode 100644 .travis.yml
 create mode 100755 scripts/R_mds.pl
 create mode 100755 scripts/mash2matrix.pl
 create mode 100644 seer-logo.png
 create mode 100755 test/6259_5_16.fa
 create mode 100644 test/assembly_locations.txt
 create mode 100644 test/map_in.txt
 copy test/{test1.txt => test1.e.txt} (51%)
 create mode 100644 test/test1.o.txt
 copy test/{test1.txt => test2.e.txt} (51%)
 rename test/{test2.txt => test2.o.txt} (99%)
 copy test/{test1.txt => test3.e.txt} (51%)
 rename test/{test3.txt => test3.o.txt} (99%)
 create mode 100644 test/test4.e.txt
 rename test/{test4.txt => test4.o.txt} (94%)
 copy test/{test1.txt => test5.e.txt} (51%)
 rename test/{test5.txt => test5.o.txt} (99%)
 rename test/{test1.txt => test6.e.txt} (51%)
 copy test/{filter_in.txt => test6.o.txt} (100%)
 delete mode 100644 test/test6.txt
 create mode 100644 test/test7.e.txt
 rename test/{test7.txt => test7.o.txt} (65%)
 create mode 100644 test/test8.e.txt
 create mode 100644 test/test8.o.txt

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