[med-svn] [freebayes] branch upstream updated (28bfd02 -> d480098)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository freebayes.

      from  28bfd02   Imported Upstream version 0.9.14+dfsg
       new  d480098   Imported Upstream version 0.9.20

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 .gitignore                             |   14 +-
 .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, 3686 insertions(+), 326 deletions(-)
 create mode 100644 CONTRIBUTORS
 create mode 100644 paper/1000G_performance_comparison.png
 create mode 100644 paper/100samples10x_0_25_both.png
 create mode 100644 paper/Makefile
 create mode 100644 paper/genome_research.bst
 create mode 100644 paper/haplotype_calling.png
 create mode 100644 paper/indel_error.png
 create mode 100644 paper/low_frequency_sensitivity.png
 create mode 100644 paper/main.aux
 create mode 100644 paper/main.bbl
 create mode 100644 paper/main.blg
 create mode 100644 paper/main.pdf
 create mode 100644 paper/main.tex
 create mode 100644 paper/miseq.png
 create mode 100644 paper/omni_errors.png
 create mode 100644 paper/references.bib
 create mode 100755 scripts/coverage_to_regions.py
 create mode 100755 scripts/freebayes-parallel
 delete mode 100644 src/version_git.h

-- 
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