[med-svn] [hisat2] branch upstream updated (ec4d09f -> b84b3bc)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository hisat2.

      from  ec4d09f   Imported Upstream version 2.0.4
       new  b84b3bc   New upstream version 2.0.5

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
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Summary of changes:
 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(-)
 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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