[med-svn] [fast5] branch upstream updated (d798d48 -> 1a33a45)

[Steffen Möller]

This is an automated email from the git hooks/post-receive script.

moeller pushed a change to branch upstream
in repository fast5.

      from  d798d48   Imported Upstream version 0.5.9
      adds  1a33a45   New upstream version 0.6.2

No new revisions were added by this update.

Summary of changes:
 .travis.Dockerfile.in             |   17 +-
 .travis.yml                       |    2 +-
 .version_files                    |    2 +-
 README.org                        |   91 +-
 VERSION                           |    2 +-
 python/.gitignore                 |    1 +
 python/Makefile                   |   20 +-
 python/bin/f5ls                   |  249 ++++
 python/bin/f5pack                 |  240 ++++
 python/fast5/.version.py.in       |    1 -
 python/fast5/__init__.py          |   10 -
 python/fast5/fast5.pyx            |  523 +++++++
 python/fast5/source/fast5.cpp     |  182 ---
 python/fast5/version.py           |    1 -
 python/setup.py                   |   86 +-
 src/.fast5_version.hpp.in         |   16 +
 src/.gitignore                    |    1 +
 src/Bit_Packer.hpp                |  152 ++
 src/File_Packer.hpp               |  982 +++++++++++++
 src/Huffman_Packer.hpp            |  357 +++++
 src/Makefile                      |   42 +-
 src/cwmap.fast5_ed_len_1.inl      |  103 ++
 src/cwmap.fast5_ed_skip_1.inl     |    4 +
 src/cwmap.fast5_ev_move_1.inl     |    6 +
 src/cwmap.fast5_ev_rel_skip_1.inl |    4 +
 src/cwmap.fast5_fq_bp_1.inl       |    7 +
 src/cwmap.fast5_fq_qv_1.inl       |   35 +
 src/cwmap.fast5_rw_1.inl          |  204 +++
 src/f5-mod.cpp                    |   14 +-
 src/f5dump.cpp                    |   96 +-
 src/f5ls-full.cpp                 |   35 +-
 src/f5ls.cpp                      |   17 +-
 src/f5pack.cpp                    |  185 +++
 src/fast5.hpp                     | 2788 ++++++++++++++++++++++++++++---------
 src/fast5_version.hpp             |   16 +
 src/hdf5-mod.cpp                  |   12 +
 src/hdf5_tools.hpp                |  316 ++++-
 src/huffman-decode.cpp            |   55 +
 src/huffman-encode.cpp            |   44 +
 src/hufftk                        |  171 +++
 src/logger.hpp                    |  378 +++++
 src/tmp.cpp                       |    7 +
 42 files changed, 6340 insertions(+), 1134 deletions(-)
 create mode 100755 python/bin/f5ls
 create mode 100755 python/bin/f5pack
 delete mode 100644 python/fast5/.version.py.in
 delete mode 100755 python/fast5/__init__.py
 create mode 100644 python/fast5/fast5.pyx
 delete mode 100644 python/fast5/source/fast5.cpp
 delete mode 100644 python/fast5/version.py
 mode change 100644 => 100755 python/setup.py
 create mode 100644 src/.fast5_version.hpp.in
 create mode 100644 src/Bit_Packer.hpp
 create mode 100644 src/File_Packer.hpp
 create mode 100644 src/Huffman_Packer.hpp
 create mode 100644 src/cwmap.fast5_ed_len_1.inl
 create mode 100644 src/cwmap.fast5_ed_skip_1.inl
 create mode 100644 src/cwmap.fast5_ev_move_1.inl
 create mode 100644 src/cwmap.fast5_ev_rel_skip_1.inl
 create mode 100644 src/cwmap.fast5_fq_bp_1.inl
 create mode 100644 src/cwmap.fast5_fq_qv_1.inl
 create mode 100644 src/cwmap.fast5_rw_1.inl
 create mode 100644 src/f5pack.cpp
 create mode 100644 src/fast5_version.hpp
 create mode 100644 src/huffman-decode.cpp
 create mode 100644 src/huffman-encode.cpp
 create mode 100755 src/hufftk
 create mode 100644 src/logger.hpp

-- 
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