[med-svn] [art-nextgen-simulation-tools] branch upstream updated (db655fc -> 3ab88b1)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository art-nextgen-simulation-tools.

      from  db655fc   Imported Upstream version 3.19.15+dfsg
       new  3ab88b1   Imported Upstream version 20160605+dfsg

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:
 ART_profiler_illumina/README                       |   28 +-
 ART_profiler_illumina/art_profiler_illumina        |  108 +-
 ChangeLog                                          |   12 +-
 GPLv3.txt                                          |  674 +++++
 Illumina_profiles/HiSeq2500L150R1filter.txt        | 1800 ++++++++++++
 Illumina_profiles/HiSeq2500L150R2filter.txt        | 1800 ++++++++++++
 Illumina_profiles/HiSeqXPCRfreeL150R1.txt          | 1812 ++++++++++++
 Illumina_profiles/HiSeqXPCRfreeL150R2.txt          | 1812 ++++++++++++
 Illumina_profiles/HiSeqXtruSeqL150R1.txt           | 1812 ++++++++++++
 Illumina_profiles/HiSeqXtruSeqL150R2.txt           | 1812 ++++++++++++
 Illumina_profiles/MiSeqv3L250R1.txt                | 3012 ++++++++++++++++++++
 Illumina_profiles/MiSeqv3L250R2.txt                | 3012 ++++++++++++++++++++
 Illumina_profiles/MiniSeqTruSeqL50.txt             |  612 ++++
 Illumina_profiles/NextSeq500v2L75R1.txt            |  912 ++++++
 Illumina_profiles/NextSeq500v2L75R2.txt            |  912 ++++++
 NEWS                                               |    3 +-
 art_454_src/art.cpp                                |   24 +-
 art_454_src/art.h                                  |   26 +-
 art_454_src/art_454.cpp                            |   24 +-
 art_454_src/readSeqFile.cpp                        |   25 +-
 art_454_src/readSeqFile.h                          |   26 +-
 art_454_src/read_profile.cpp                       |   26 +-
 art_454_src/read_profile.h                         |   26 +-
 art_454_src/samRead.cpp                            |   23 +-
 art_454_src/samRead.h                              |   24 +-
 art_454_src/seqRead.cpp                            |   26 +-
 art_454_src/seqRead.h                              |   26 +-
 art_SOLiD_src/art.cpp                              |   26 +-
 art_SOLiD_src/art.h                                |   26 +-
 art_SOLiD_src/art_SOLiD.cpp                        |   27 +-
 art_SOLiD_src/readSeqFile.cpp                      |   25 +-
 art_SOLiD_src/readSeqFile.h                        |   26 +-
 art_SOLiD_src/read_SOLiD.cpp                       |   26 +-
 art_SOLiD_src/read_SOLiD.h                         |   26 +-
 art_SOLiD_src/samRead.cpp                          |   23 +-
 art_SOLiD_src/samRead.h                            |   24 +-
 art_SOLiD_src/utility.hpp                          |   26 +-
 art_illumina_README                                |  235 +-
 art_illumina_src/art.h                             |   25 +-
 art_illumina_src/art_illumina.cpp                  |  250 +-
 .../{art_illumina.cpp => art_illumina_m.cpp}       |  246 +-
 art_illumina_src/art_qual_scale.cpp                |   97 +-
 art_illumina_src/empdist.cpp                       |   65 +-
 art_illumina_src/empdist.h                         |   18 +-
 art_illumina_src/readSeqFile.cpp                   |   25 +-
 art_illumina_src/readSeqFile.h                     |   26 +-
 art_illumina_src/samRead.cpp                       |   23 +-
 art_illumina_src/samRead.h                         |   24 +-
 art_illumina_src/seqRead.cpp                       |   83 +-
 art_illumina_src/seqRead.h                         |   48 +-
 configure.ac                                       |    3 +-
 examples/run_test_examples_illumina.sh             |   29 +-
 52 files changed, 21378 insertions(+), 483 deletions(-)
 create mode 100644 GPLv3.txt
 create mode 100644 Illumina_profiles/HiSeq2500L150R1filter.txt
 create mode 100644 Illumina_profiles/HiSeq2500L150R2filter.txt
 create mode 100644 Illumina_profiles/HiSeqXPCRfreeL150R1.txt
 create mode 100644 Illumina_profiles/HiSeqXPCRfreeL150R2.txt
 create mode 100644 Illumina_profiles/HiSeqXtruSeqL150R1.txt
 create mode 100644 Illumina_profiles/HiSeqXtruSeqL150R2.txt
 create mode 100644 Illumina_profiles/MiSeqv3L250R1.txt
 create mode 100644 Illumina_profiles/MiSeqv3L250R2.txt
 create mode 100644 Illumina_profiles/MiniSeqTruSeqL50.txt
 create mode 100644 Illumina_profiles/NextSeq500v2L75R1.txt
 create mode 100644 Illumina_profiles/NextSeq500v2L75R2.txt
 copy art_illumina_src/{art_illumina.cpp => art_illumina_m.cpp} (77%)

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