[med-svn] [hisat2] 04/07: Merge tag 'upstream/2.0.5'

[Andreas Tille]

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tille pushed a commit to branch master
in repository hisat2.

commit 885cc2482d32e3e46b7c709ca3076ccf02fc56cf
Merge: 40902b2 b84b3bc
Author: Andreas Tille <tille at debian.org>
Date:   Fri Dec 9 13:44:30 2016 +0100

    Merge tag 'upstream/2.0.5'
    
    Upstream version 2.0.5

 MANUAL                                             |   86 +-
 MANUAL.markdown                                    |  129 +-
 VERSION                                            |    2 +-
 aligner_seed_policy.cpp                            |    2 +-
 aln_sink.h                                         |    8 +-
 doc/manual.inc.html                                |   94 +-
 gfm.h                                              |   12 +-
 gp.h                                               |   65 +
 hi_aligner.h                                       |  483 ++-
 hisat2.cpp                                         |  146 +-
 hisat2_build_genotype_genome.py                    |   89 +-
 hisat2_inspect.cpp                                 |    3 +-
 hisat2_test_HLA_genotyping.py                      | 3547 ++++++++++++++------
 hisat_bp.cpp                                       |    4 +-
 ...ct_HLA_vars.py => hisatgenotype_extract_vars.py |  587 +++-
 hisatgenotype_typing.py                            | 1688 ++++++++++
 ...otyping.py => old_hisat2_test_HLA_genotyping.py |   83 +-
 opts.h                                             |    3 +
 pat.cpp                                            |   16 +
 ref_read.cpp                                       |   14 +
 sam.h                                              |    2 +-
 spliced_aligner.h                                  |  324 +-
 tp.h                                               |   69 +-
 23 files changed, 5519 insertions(+), 1937 deletions(-)

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