[med-svn] [seer] 11/13: Merge tag 'upstream/1.1.0'
Andreas Tille
tille at debian.org
Thu Apr 14 09:49:56 UTC 2016
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tille pushed a commit to branch master
in repository seer.
commit ef761c80c587716de857f4459b428be422a17076
Merge: d9bb507 e7649c6
Author: Andreas Tille <tille at debian.org>
Date: Thu Apr 14 11:46:56 2016 +0200
Merge tag 'upstream/1.1.0'
Upstream version 1.1.0
.gitignore | 45 +
.gitmodules | 3 +
LICENSE | 340 +++
Makefile | 19 +
README.md | 91 +
debian/README.Debian | 12 -
debian/changelog | 11 -
debian/compat | 1 -
debian/control | 38 -
debian/copyright | 26 -
debian/examples | 1 -
debian/manpages | 1 -
debian/mans/blast_top_hits.1 | 28 -
debian/mans/combineKmers.1 | 26 -
debian/mans/filter_seer.1 | 41 -
debian/mans/kmds.1 | 74 -
debian/mans/map_back.1 | 26 -
debian/mans/seer.1 | 75 -
debian/patches/fix_lib_location.patch | 20 -
debian/patches/hardening.patch | 39 -
debian/patches/pthread_versus_hardening.patch | 20 -
debian/patches/series | 3 -
debian/rules | 21 -
debian/source/format | 1 -
debian/upstream/metadata | 8 -
debian/watch | 3 -
example_wrapper.py | 185 ++
scripts/blast_top_hits.pl | 130 ++
src/Makefile | 84 +
src/combineCmdLine.cpp | 63 +
src/combineInit.cpp | 47 +
src/combineKmers.cpp | 104 +
src/combineKmers.hpp | 25 +
src/covar.cpp | 28 +
src/covar.hpp | 27 +
src/fasta.cpp | 113 +
src/fasta.hpp | 42 +
src/filterCmdLine.cpp | 160 ++
src/filter_seer.cpp | 148 ++
src/filter_seer.hpp | 34 +
src/kmds.hpp | 39 +
src/kmdsCmdLine.cpp | 95 +
src/kmdsMain.cpp | 264 +++
src/kmdsStruct.cpp | 161 ++
src/kmer.cpp | 149 ++
src/kmer.hpp | 55 +
src/linearFunction.cpp | 39 +
src/linkFunction.hpp | 72 +
src/logitFunction.cpp | 76 +
src/mapCmdLine.cpp | 67 +
src/mapMain.cpp | 157 ++
src/map_back.hpp | 43 +
src/sample.cpp | 44 +
src/sample.hpp | 31 +
src/seer.hpp | 45 +
src/seerBinaryAssoc.cpp | 199 ++
src/seerChiFilter.cpp | 127 +
src/seerCmdLine.cpp | 102 +
src/seerCommon.cpp | 243 ++
src/seerContinuousAssoc.cpp | 100 +
src/seerErr.cpp | 14 +
src/seerFilter.cpp | 82 +
src/seerIO.cpp | 317 +++
src/seerMain.cpp | 209 ++
src/seercommon.hpp | 117 +
src/significant_kmer.cpp | 133 ++
src/significant_kmer.hpp | 73 +
test/Makefile | 10 +
test/example.pheno | 3069 +++++++++++++++++++++++++
test/example_kmers.gz | Bin 0 -> 63488 bytes
test/generate_test.pl | 49 +
test/subset.pheno | 200 ++
72 files changed, 8069 insertions(+), 475 deletions(-)
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