[med-svn] [freebayes] branch upstream updated (d480098 -> 492c86d)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository freebayes.

      from  d480098   Imported Upstream version 0.9.20
       new  492c86d   Imported Upstream version 1.0.2

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:
 .gitmodules                           |   6 +
 .travis.yml                           |  14 +
 Makefile                              |   7 +-
 README.md                             |  16 +-
 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
 51 files changed, 1864 insertions(+), 781 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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