[med-svn] [fastqtl] 03/04: Merge tag 'upstream/2.184+dfsg'

[Dylan Aïssi]

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bob.dybian-guest pushed a commit to branch master
in repository fastqtl.

commit 0b964d008f0158c40f0f11b6856e9a3992b8cf4e
Merge: 27ca6a5 8cf0631
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Mon May 2 23:44:30 2016 +0200

    Merge tag 'upstream/2.184+dfsg'
    
    Upstream version 2.184+dfsg

 INSTALL                                    | 142 ++++++
 LICENCE                                    | 621 ++++++++++++++++++++++++
 Makefile                                   |  79 ++++
 README                                     |   1 +
 doc/img/fastqtl_checks.jpg                 | Bin 0 -> 188036 bytes
 doc/img/fastqtl_screenshot_nominal.jpg     | Bin 0 -> 274581 bytes
 doc/img/fastqtl_screenshot_permutation.jpg | Bin 0 -> 399258 bytes
 doc/index.html                             |  27 ++
 doc/pages/cis_mapping.html                 |  35 ++
 doc/pages/cis_nominal.html                 | 250 ++++++++++
 doc/pages/cis_permutation.html             | 354 ++++++++++++++
 doc/pages/footer.html                      |  15 +
 doc/pages/format_bed.html                  |  71 +++
 doc/pages/format_cov.html                  |  52 ++
 doc/pages/format_vcf.html                  |  63 +++
 doc/pages/header.html                      |  13 +
 doc/pages/homepage.html                    |  56 +++
 doc/pages/install.html                     |  97 ++++
 doc/pages/leftmenu.html                    |  37 ++
 doc/pages/options.html                     | 247 ++++++++++
 doc/pages/template.html                    |  51 ++
 doc/script/print_last_modif_date.js        |   3 +
 doc/style/default.css                      | 228 +++++++++
 example/covariates.txt.gz                  | Bin 0 -> 3379 bytes
 example/genotypes.vcf.gz                   | Bin 0 -> 15890106 bytes
 example/genotypes.vcf.gz.tbi               | Bin 0 -> 26376 bytes
 example/interaction.txt                    | 373 +++++++++++++++
 example/phenotypes.bed.gz                  | Bin 0 -> 404725 bytes
 example/phenotypes.bed.gz.tbi              | Bin 0 -> 3703 bytes
 script/calulateNominalPvalueThresholds.R   |  33 ++
 src/analysisMapping.cpp                    | 142 ++++++
 src/analysisNominal.cpp                    |  69 +++
 src/analysisPermutation.cpp                | 136 ++++++
 src/analysisPermutationInteraction.cpp     | 126 +++++
 src/analysisPermutationPerGroup.cpp        | 160 +++++++
 src/analysisPermutationSequence.cpp        | 135 ++++++
 src/commands.cpp                           |  52 ++
 src/data.h                                 | 210 +++++++++
 src/df.cpp                                 | 100 ++++
 src/fastQTL.cpp                            | 290 ++++++++++++
 src/management.cpp                         | 252 ++++++++++
 src/mle.cpp                                |  88 ++++
 src/readCovariates.cpp                     |  77 +++
 src/readGenotypes.cpp                      | 117 +++++
 src/readGroups.cpp                         |  54 +++
 src/readInclusionsExclusions.cpp           |  89 ++++
 src/readInteractions.cpp                   |  51 ++
 src/readPhenotypes.cpp                     | 119 +++++
 src/readThresholds.cpp                     |  53 +++
 src/region.h                               |  66 +++
 src/residualizer.cpp                       | 142 ++++++
 src/residualizer.h                         |  53 +++
 src/utils/ranker.h                         | 224 +++++++++
 src/utils/tabix.cpp                        | 107 +++++
 src/utils/tabix.hpp                        |  41 ++
 src/utils/utils.cpp                        | 731 +++++++++++++++++++++++++++++
 src/utils/utils.h                          | 312 ++++++++++++
 57 files changed, 6844 insertions(+)

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