[med-svn] [hisat2] branch master updated (9080a1b -> cd96070)

[Andreas Tille]

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tille pushed a change to branch master
in repository hisat2.

      from  9080a1b   set TZ=UTC
       new  ccc18bd   Architecture: amd64 kfreebsd-amd64
       new  40902b2     * d/watch:      - version=4      - xz compression
       new  b84b3bc   New upstream version 2.0.5
       new  885cc24   Merge tag 'upstream/2.0.5'
       new  d6393b7   New upstream version
       new  68d16f1   debhelper 10
       new  cd96070   Upload to unstable

The 7 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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Summary of changes:
 MANUAL                                             |   86 +-
 MANUAL.markdown                                    |  129 +-
 VERSION                                            |    2 +-
 aligner_seed_policy.cpp                            |    2 +-
 aln_sink.h                                         |    8 +-
 debian/changelog                                   |   13 +
 debian/compat                                      |    2 +-
 debian/control                                     |    4 +-
 debian/watch                                       |    4 +-
 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 +-
 27 files changed, 5537 insertions(+), 1942 deletions(-)
 create mode 100644 gp.h
 rename hisat2_extract_HLA_vars.py => hisatgenotype_extract_vars.py (60%)
 create mode 100755 hisatgenotype_typing.py
 copy hisat2_test_HLA_genotyping.py => old_hisat2_test_HLA_genotyping.py (96%)

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