[med-svn] [freebayes] branch master updated (7233aa1 -> a06c13f)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository freebayes.

      from  7233aa1   Upload to new
      adds  be3cf11   Add missing license statements
      adds  a0624d4   New upstream version 1.1.0
      adds  3937761   Merge tag 'upstream/1.1.0'
      adds  dbf5149   Changes to build new upstream version
      adds  89af2b7   Fix copyright
      adds  9cb4df5   Commit as uploaded
      adds  a06c13f   Commit as freebayes was uploaded

No new revisions were added by this update.

Summary of changes:
 .gitmodules                            |   9 +-
 README.md                              |   8 +-
 debian/copyright                       | 420 ++++++++++++++++++++++
 python/allelebayes.py                  |   2 +
 python/multiset.py                     |   2 +-
 scripts/bgziptabix                     |  13 +
 scripts/fasta_generate_regions.py      |   2 +-
 scripts/freebayes-parallel             |   4 +-
 scripts/sam_add_rg.pl                  |   2 +-
 src/Allele.h                           |   7 +-
 src/AlleleParser.cpp                   | 633 ++++++++++++++++++++-------------
 src/AlleleParser.h                     |  63 ++--
 src/Fasta.cpp                          |  24 +-
 src/Fasta.h                            |   3 +
 src/Genotype.cpp                       |   2 +-
 src/LeftAlign.cpp                      | 115 +++---
 src/LeftAlign.h                        |  94 ++++-
 src/Makefile                           |  40 ++-
 src/NonCall.cpp                        |  15 +-
 src/NonCall.h                          |   2 +
 src/Parameters.cpp                     |   8 +
 src/Parameters.h                       |   1 +
 src/ResultData.cpp                     |  56 ++-
 src/ResultData.h                       |   8 +-
 src/bamleftalign.cpp                   |  69 ++--
 src/freebayes.cpp                      |  23 +-
 test/Makefile                          |   2 +-
 test/region-and-target-handling.t      | 104 ------
 test/t/00_region_and_target_handling.t | 145 ++++++++
 test/t/01_call_variants.t              |  12 +-
 test/t/02_multi_bam.t                  |  88 +++++
 test/t/03_reference_bases.t            |  56 +++
 32 files changed, 1486 insertions(+), 546 deletions(-)
 create mode 100755 scripts/bgziptabix
 delete mode 100644 test/region-and-target-handling.t
 create mode 100644 test/t/00_region_and_target_handling.t
 mode change 100644 => 100755 test/t/01_call_variants.t
 create mode 100755 test/t/02_multi_bam.t
 create mode 100644 test/t/03_reference_bases.t

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