[med-svn] [freebayes] branch master updated (50887db -> 854d6a5)

[Andreas Tille]

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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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