[med-svn] [seer] 02/07: Merge tag 'upstream/1.1.1'

[Andreas Tille]

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tille pushed a commit to branch master
in repository seer.

commit b4f9172bd7a7e2533a7a2e6652aebf7b5be51251
Merge: cc79782 954fcd0
Author: Andreas Tille <tille at debian.org>
Date:   Thu Apr 14 11:51:54 2016 +0200

    Merge tag 'upstream/1.1.1'
    
    Upstream version 1.1.1

 .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(-)

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