[med-svn] [art-nextgen-simulation-tools] branch master updated (6976727 -> 53faee2)

[Andreas Tille]

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

      from  6976727   Better hardening and upload to new
       new  3ab88b1   Imported Upstream version 20160605+dfsg
       new  f16a1bd   Merge tag 'upstream/20160605+dfsg'
       new  42a32ff   New upstream version
       new  53faee2   Adapt patch

The 4 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 +-
 debian/changelog                                   |    4 +-
 debian/patches/adapt_path_to_perl_scripts.patch    |   12 +-
 examples/run_test_examples_illumina.sh             |   29 +-
 54 files changed, 21386 insertions(+), 491 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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