[med-svn] [freebayes] 04/04: Merge tag 'upstream/0.9.20'

[Andreas Tille]

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tille pushed a commit to branch master
in repository freebayes.

commit 5d04db52934c2c9f3e8bb86ff86310c5aba9cb90
Merge: 0b191b0 d480098
Author: Andreas Tille <tille at debian.org>
Date:   Sun Feb 1 08:38:47 2015 +0100

    Merge tag 'upstream/0.9.20'
    
    Upstream version 0.9.20
    
    Conflicts:
    	.gitignore

 .gitignore                             |    6 +-
 .gitmodules                            |    2 +-
 CONTRIBUTORS                           |    7 +
 Makefile                               |    9 +-
 README.md                              |  126 ++-
 paper/1000G_performance_comparison.png |  Bin 0 -> 61887 bytes
 paper/100samples10x_0_25_both.png      |  Bin 0 -> 89862 bytes
 paper/Makefile                         |   10 +
 paper/genome_research.bst              | 1620 ++++++++++++++++++++++++++++++++
 paper/haplotype_calling.png            |  Bin 0 -> 175436 bytes
 paper/indel_error.png                  |  Bin 0 -> 44097 bytes
 paper/low_frequency_sensitivity.png    |  Bin 0 -> 138914 bytes
 paper/main.aux                         |  121 +++
 paper/main.bbl                         |  170 ++++
 paper/main.blg                         |   49 +
 paper/main.pdf                         |  Bin 0 -> 846894 bytes
 paper/main.tex                         |  664 +++++++++++++
 paper/miseq.png                        |  Bin 0 -> 80796 bytes
 paper/omni_errors.png                  |  Bin 0 -> 94711 bytes
 paper/references.bib                   |  321 +++++++
 scripts/coverage_to_regions.py         |   51 +
 scripts/fasta_generate_regions.py      |    8 +-
 scripts/freebayes-parallel             |   40 +
 src/Allele.cpp                         |    4 +
 src/AlleleParser.cpp                   |  447 +++++----
 src/AlleleParser.h                     |   10 +-
 src/BedReader.cpp                      |    5 +
 src/BedReader.h                        |    2 +-
 src/Genotype.cpp                       |   47 +-
 src/GenotypePriors.cpp                 |   11 +-
 src/Makefile                           |   66 +-
 src/Marginals.cpp                      |   10 +-
 src/Parameters.cpp                     |  115 ++-
 src/Parameters.h                       |    1 +
 src/ResultData.cpp                     |   28 +-
 src/freebayes.cpp                      |   44 +-
 src/version_git.h                      |    4 -
 src/version_release.txt                |    6 +-
 38 files changed, 3687 insertions(+), 317 deletions(-)


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