[med-svn] [fast5] branch master updated (c66dbbd -> c435e52)

[Steffen Möller]

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

moeller pushed a change to branch master
in repository fast5.

      from  c66dbbd   Added references to registries.
       new  1a33a45   New upstream version 0.6.2
       new  0276783   Updated version 0.6.2 from 'upstream/0.6.2'
       new  c435e52   Getting 0.6.2 to build binaries.

The 3 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
been added to this reference.


Summary of changes:
 .travis.Dockerfile.in             |   17 +-
 .travis.yml                       |    2 +-
 .version_files                    |    2 +-
 README.org                        |   91 +-
 VERSION                           |    2 +-
 debian/changelog                  |   14 +
 debian/patches/functional.patch   |   12 +
 debian/patches/hdf5include.patch  |   13 +
 debian/patches/rpath.patch        |   22 +-
 debian/patches/series             |    6 +-
 debian/rules                      |    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 +
 48 files changed, 6396 insertions(+), 1147 deletions(-)
 create mode 100644 debian/patches/functional.patch
 create mode 100644 debian/patches/hdf5include.patch
 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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