[med-svn] [eagle] 03/03: Merge tag 'upstream/2.3'

[Dylan Aïssi]

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

commit f86030092aad02bbd6681082b955e3927740b257
Merge: 8931cf0 8715418
Author: Dylan Aïssi <bob.dybian at gmail.com>
Date:   Sun Sep 18 23:05:47 2016 +0200

    Merge tag 'upstream/2.3'
    
    Upstream version 2.3

 .gitignore                             |    2 +
 README.md                              |    7 +
 example/EUR_test.bed                   |  400 ++++
 example/EUR_test.bim                   | 2000 ++++++++++++++++++
 example/EUR_test.fam                   |  379 ++++
 example/EUR_test.vcf.gz                |  Bin 0 -> 193569 bytes
 example/example.log                    |  194 ++
 example/example_ref.log                |   79 +
 example/example_vcf.log                |  177 ++
 example/phased.haps.gz                 |  Bin 0 -> 194442 bytes
 example/phased.sample                  |  381 ++++
 example/phased.vcf.gz                  |  Bin 0 -> 200389 bytes
 example/ref.bcf                        |  Bin 0 -> 59136 bytes
 example/ref.bcf.csi                    |  Bin 0 -> 1185 bytes
 example/run_example.sh                 |   19 +
 example/run_example_ref.sh             |    9 +
 example/run_example_vcf.sh             |   17 +
 example/target.phased.vcf.gz           |  Bin 0 -> 21049 bytes
 example/target.vcf.gz                  |  Bin 0 -> 20835 bytes
 example/target.vcf.gz.tbi              |  Bin 0 -> 1275 bytes
 src/COPYING                            |  675 ++++++
 src/DipTreePBWT.cpp                    |  611 ++++++
 src/DipTreePBWT.hpp                    |  169 ++
 src/Eagle.cpp                          | 3576 ++++++++++++++++++++++++++++++++
 src/Eagle.hpp                          |  209 ++
 src/EagleImpMiss.cpp                   |  286 +++
 src/EagleMain.cpp                      |  620 ++++++
 src/EaglePBWT.cpp                      |  744 +++++++
 src/EagleParams.cpp                    |  379 ++++
 src/EagleParams.hpp                    |   83 +
 src/FileUtils.cpp                      |  215 ++
 src/FileUtils.hpp                      |   94 +
 src/GenoData.cpp                       |  845 ++++++++
 src/GenoData.hpp                       |  140 ++
 src/HapHedge.cpp                       |  599 ++++++
 src/HapHedge.hpp                       |  133 ++
 src/LapackConst.hpp                    |   76 +
 src/Makefile                           |  107 +
 src/MapInterpolater.cpp                |   83 +
 src/MapInterpolater.hpp                |   40 +
 src/MemoryUtils.cpp                    |   40 +
 src/MemoryUtils.hpp                    |   45 +
 src/NumericUtils.cpp                   |  108 +
 src/NumericUtils.hpp                   |   52 +
 src/StaticMultimap.cpp                 |  114 +
 src/StaticMultimap.hpp                 |   56 +
 src/StringUtils.cpp                    |  151 ++
 src/StringUtils.hpp                    |   45 +
 src/SyncedVcfData.cpp                  |  520 +++++
 src/SyncedVcfData.hpp                  |   76 +
 src/Timer.cpp                          |   46 +
 src/Timer.hpp                          |   34 +
 src/Types.hpp                          |   31 +
 src/Version.hpp                        |   25 +
 tables/README.txt                      |    3 +
 tables/genetic_map_hg19_example.txt.gz |  Bin 0 -> 718229 bytes
 56 files changed, 14694 insertions(+)

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