[med-svn] [art-nextgen-simulation-tools] 02/04: Merge tag 'upstream/20160605+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository art-nextgen-simulation-tools.

commit f16a1bdc481c00adc88e5d5a6c3a84bd65f97cf8
Merge: 6976727 3ab88b1
Author: Andreas Tille <tille at debian.org>
Date:   Sun Jul 3 22:49:40 2016 +0200

    Merge tag 'upstream/20160605+dfsg'
    
    Upstream version 20160605+dfsg

 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(-)

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