[med-svn] [seer] branch master updated (cc79782 -> 2ff03de)

[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  cc79782   Moved packaging from SVN to Git
       new  954fcd0   Imported Upstream version 1.1.1
       new  b4f9172   Merge tag 'upstream/1.1.1'
       new  98f2882   New upstream version
       new  d29c13c   Adapt patches
       new  d2928eb   Upstream added -pthread where necessary
       new  5608fa7   Add notice to log if test fails but continue building anyway
       new  2ff03de   Upload to unstable

The 7 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:
 .gitmodules                                   |    2 +-
 Makefile                                      |    1 -
 README.md                                     |   39 +-
 debian/README.source                          |    6 +
 debian/changelog                              |    6 +-
 debian/patches/fix_lib_location.patch         |   22 +-
 debian/patches/hardening.patch                |   22 +-
 debian/patches/pthread_versus_hardening.patch |   20 -
 debian/patches/series                         |    1 -
 debian/rules                                  |    7 +-
 scripts/hits_to_fastq.pl                      |   85 +
 scripts/mapping_to_phandango.pl               |  106 +
 scripts/reformat_output.pl                    |   88 +
 src/Makefile                                  |   18 +-
 src/filter_seer.cpp                           |    7 +-
 src/kmdsCmdLine.cpp                           |    5 +-
 src/kmdsMain.cpp                              |   35 +-
 src/kmdsStruct.cpp                            |    7 +-
 src/kmer.cpp                                  |   22 +-
 src/kmer.hpp                                  |    7 +-
 src/mapMain.cpp                               |    7 +-
 src/seer.hpp                                  |    3 +-
 src/seerBinaryAssoc.cpp                       |  166 +-
 src/seerChiFilter.cpp                         |   53 +-
 src/seerCmdLine.cpp                           |    2 +-
 src/seerCommon.cpp                            |    7 +-
 src/seerContinuousAssoc.cpp                   |   13 +-
 src/seerFilter.cpp                            |   42 +-
 src/seerIO.cpp                                |  104 +-
 src/seerMain.cpp                              |   35 +-
 src/seercommon.hpp                            |   16 +-
 src/significant_kmer.cpp                      |   61 +-
 src/significant_kmer.hpp                      |   14 +
 test/Makefile                                 |    4 +-
 test/all_structure_new                        |  Bin 0 -> 75800 bytes
 test/all_structure_new.samples                | 3069 +++++++++++++++++++++++++
 test/covariates.txt                           |  200 ++
 test/filter_in.txt                            |  175 ++
 test/run_test.pl                              |   45 +
 test/subset.cont.pheno                        |  200 ++
 test/test1.txt                                |    4 +
 test/test2.txt                                |  178 ++
 test/test3.txt                                |   99 +
 test/test4.txt                                |   20 +
 test/test5.txt                                |  182 ++
 test/test6.txt                                |  178 ++
 test/test7.txt                                |  155 ++
 47 files changed, 5333 insertions(+), 205 deletions(-)
 create mode 100644 debian/README.source
 delete mode 100644 debian/patches/pthread_versus_hardening.patch
 create mode 100755 scripts/hits_to_fastq.pl
 create mode 100755 scripts/mapping_to_phandango.pl
 create mode 100755 scripts/reformat_output.pl
 create mode 100644 test/all_structure_new
 create mode 100644 test/all_structure_new.samples
 create mode 100644 test/covariates.txt
 create mode 100644 test/filter_in.txt
 create mode 100755 test/run_test.pl
 create mode 100644 test/subset.cont.pheno
 create mode 100644 test/test1.txt
 create mode 100644 test/test2.txt
 create mode 100644 test/test3.txt
 create mode 100644 test/test4.txt
 create mode 100644 test/test5.txt
 create mode 100644 test/test6.txt
 create mode 100644 test/test7.txt

-- 
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