[med-svn] [andi] branch upstream updated (abc0e9a -> 8ce73df)

[Fabian Klötzl]

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kloetzl-guest pushed a change to branch upstream
in repository andi.

      from  abc0e9a   Imported Upstream version 0.9.5
      adds  a88fbdf   Imported Upstream version 0.9.6
      adds  8ce73df   Imported Upstream version 0.9.6.1

No new revisions were added by this update.

Summary of changes:
 .clang-format               |   9 ++
 .travis.yml                 |  47 +++---
 Makefile.am                 |   6 +-
 README.md                   |   6 +-
 andi-manual.pdf             | Bin 423356 -> 425545 bytes
 configure.ac                |  17 +-
 docs/andi.1.in              |  13 +-
 docs/manual/andi-manual.tex |  17 +-
 opt/psufsort/Makefile.am    |   2 +-
 src/Makefile.am             |   7 +-
 src/andi.c                  | 326 ++++++++++++++++++++-------------------
 src/dist_hack.h             |  46 +++---
 src/esa.c                   | 368 +++++++++++++++++++++-----------------------
 src/esa.h                   |  19 ++-
 src/global.h                |  21 ++-
 src/io.c                    | 161 +++++++++----------
 src/io.h                    |  24 +--
 src/model.c                 | 255 ++++++++++++++++++++++++++++++
 src/model.h                 |  64 ++++++++
 src/process.c               | 336 ++++++++++++++++++----------------------
 src/process.h               |   6 +-
 src/sequence.c              | 203 +++++++++++-------------
 src/sequence.h              |  20 +--
 test/Makefile.am            |   6 +-
 test/test_extra.sh          |   6 +-
 test/test_fasta.cxx         |  26 +++-
 test/test_join.sh           |   6 +-
 test/test_random.sh         |  54 ++++++-
 test/test_seq.c             |   4 +-
 29 files changed, 1218 insertions(+), 857 deletions(-)
 create mode 100644 .clang-format
 create mode 100644 src/model.c
 create mode 100644 src/model.h

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