[med-svn] [freebayes] branch master updated (50887db -> 854d6a5)
Andreas Tille
tille at debian.org
Wed Jun 22 12:26:24 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository freebayes.
from 50887db Add comment that packaging of vcslib has started
new 492c86d Imported Upstream version 1.0.2
new 2e172cf Merge tag 'upstream/1.0.2'
new 4e9f7c0 New upstream version
new f09cec1 cme fix dpkg-control
new 854d6a5 Debian Med team maintenance
The 5 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:
.gitmodules | 6 +
.travis.yml | 14 +
Makefile | 7 +-
README.md | 16 +-
debian/changelog | 2 +-
debian/control | 17 +-
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
53 files changed, 1875 insertions(+), 789 deletions(-)
create mode 100644 .travis.yml
delete mode 100644 paper/main.pdf
create mode 100644 src/NonCall.cpp
create mode 100644 src/NonCall.h
create mode 100644 test/Makefile
create mode 100644 test/region-and-target-handling.t
create mode 100644 test/splice/1:883884-887618.bam
create mode 100644 test/splice/1:883884-887618.bam.bai
create mode 100644 test/splice/1:883884-887618.fa
create mode 100644 test/splice/1:883884-887618.fa.fai
create mode 100644 test/t/01_call_variants.t
create mode 100644 test/tiny/1read.bam
create mode 100644 test/tiny/1read.bam.bai
create mode 100644 test/tiny/NA12878.chr22.tiny.bam
create mode 100644 test/tiny/NA12878.chr22.tiny.bam.bai
create mode 100644 test/tiny/NA12878.chr22.tiny.giab.vcf
create mode 100644 test/tiny/q with spaces.fa
create mode 100644 test/tiny/q with spaces.fa.fai
create mode 100644 test/tiny/q with spaces.regions
create mode 100644 test/tiny/q.fa
create mode 100644 test/tiny/q.fa.fai
create mode 100644 test/tiny/q.regions
create mode 100644 test/tiny/q.vcf.gz
create mode 100644 test/tiny/q.vcf.gz.tbi
create mode 100644 test/tiny/q_spiked.vcf.gz
create mode 100644 test/tiny/q_spiked.vcf.gz.tbi
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