[med-svn] [freebayes] 02/05: Merge tag 'upstream/1.0.2'

[Andreas Tille]

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tille pushed a commit to branch master
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commit 2e172cff23fb3da6243f1dfcd493112e95ef9e9c
Merge: 50887db 492c86d
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jun 22 14:24:37 2016 +0200

    Merge tag 'upstream/1.0.2'
    
    Upstream version 1.0.2

 .gitmodules                           |   6 +
 .travis.yml                           |  14 +
 Makefile                              |   7 +-
 README.md                             |  16 +-
 paper/main.blg                        |   2 +-
 paper/main.pdf                        | Bin 846894 -> 0 bytes
 scripts/freebayes-parallel            |   4 +-
 src/AlleleParser.cpp                  | 752 +++++++++++++++-------------------
 src/AlleleParser.h                    |  23 +-
 src/DataLikelihood.cpp                | 196 ++++++---
 src/DataLikelihood.h                  |  18 +
 src/Genotype.cpp                      |  18 +-
 src/Genotype.h                        |   4 +-
 src/IndelAllele.cpp                   |   6 +-
 src/IndelAllele.h                     |   5 +-
 src/LeftAlign.cpp                     |  34 +-
 src/Makefile                          |   6 +-
 src/Multinomial.cpp                   |  10 +
 src/Multinomial.h                     |   2 +
 src/NonCall.cpp                       |  86 ++++
 src/NonCall.h                         |  48 +++
 src/Parameters.cpp                    | 105 +++--
 src/Parameters.h                      |   7 +-
 src/ResultData.cpp                    |  68 +++
 src/ResultData.h                      |   8 +-
 src/Sample.cpp                        |   2 +-
 src/Sample.h                          |   2 -
 src/freebayes.cpp                     | 385 ++++++++---------
 src/version_release.txt               |   6 +-
 test/Makefile                         |  15 +
 test/region-and-target-handling.t     | 104 +++++
 test/splice/1:883884-887618.bam       | Bin 0 -> 22589 bytes
 test/splice/1:883884-887618.bam.bai   | Bin 0 -> 288 bytes
 test/splice/1:883884-887618.fa        |  64 +++
 test/splice/1:883884-887618.fa.fai    |   1 +
 test/t/01_call_variants.t             | 110 +++++
 test/tiny/1read.bam                   | Bin 0 -> 636 bytes
 test/tiny/1read.bam.bai               | Bin 0 -> 96 bytes
 test/tiny/NA12878.chr22.tiny.bam      | Bin 0 -> 287213 bytes
 test/tiny/NA12878.chr22.tiny.bam.bai  | Bin 0 -> 96 bytes
 test/tiny/NA12878.chr22.tiny.giab.vcf |  89 ++++
 test/tiny/q with spaces.fa            | 207 ++++++++++
 test/tiny/q with spaces.fa.fai        |   1 +
 test/tiny/q with spaces.regions       |   3 +
 test/tiny/q.fa                        | 207 ++++++++++
 test/tiny/q.fa.fai                    |   1 +
 test/tiny/q.regions                   |   3 +
 test/tiny/q.vcf.gz                    | Bin 0 -> 4305 bytes
 test/tiny/q.vcf.gz.tbi                | Bin 0 -> 102 bytes
 test/tiny/q_spiked.vcf.gz             | Bin 0 -> 2378 bytes
 test/tiny/q_spiked.vcf.gz.tbi         | Bin 0 -> 91 bytes
 51 files changed, 1864 insertions(+), 781 deletions(-)


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