[med-svn] [seer] branch upstream updated (e7649c6 -> 954fcd0)

[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  e7649c6   Imported Upstream version 1.1.0
       new  954fcd0   Imported Upstream version 1.1.1

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:
 .gitmodules                     |    2 +-
 Makefile                        |    1 -
 README.md                       |   39 +-
 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 ++
 40 files changed, 5294 insertions(+), 160 deletions(-)
 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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