[med-svn] [freebayes] branch master updated (e7e5c2e -> 5d04db5)
Andreas Tille
tille at debian.org
Sun Feb 1 07:40:32 UTC 2015
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tille pushed a change to branch master
in repository freebayes.
from e7e5c2e Use Debian packaged bamtools; TODO: Package https://github.com/ekg/vcflib
new dab2e3b Bamtools is now an empty directory in upstream source tarball - so no point in removing it any more
new 0b191b0 New upstream source
new d480098 Imported Upstream version 0.9.20
new 5d04db5 Merge tag 'upstream/0.9.20'
The 4 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 | 6 +-
.gitmodules | 2 +-
CONTRIBUTORS | 7 +
Makefile | 9 +-
README.md | 126 ++-
debian/changelog | 2 +-
debian/copyright | 1 -
debian/watch | 2 +-
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 +-
41 files changed, 3689 insertions(+), 320 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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