[med-svn] [freebayes] branch upstream updated (492c86d -> a0624d4)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository freebayes.

      from  492c86d   Imported Upstream version 1.0.2
      adds  a0624d4   New upstream version 1.1.0

No new revisions were added by this update.

Summary of changes:
 .gitmodules                            |   9 +-
 README.md                              |   8 +-
 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 +++
 31 files changed, 1066 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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