[med-svn] [fast5] branch upstream updated (1a33a45 -> 6198cc7)

[Afif Elghraoui]

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

afif pushed a change to branch upstream
in repository fast5.

      from  1a33a45   New upstream version 0.6.2
       new  6198cc7   New upstream version 0.6.3

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
been added to this reference.


Summary of changes:
 .gitignore                                         |    2 +
 .travis.yml                                        |    2 +-
 Doxyfile                                           | 2479 ++++++++++++++++++++
 README.org                                         |    2 +-
 {src => include}/fast5.hpp                         |   24 +-
 {src => include/fast5}/Bit_Packer.hpp              |    0
 {src => include/fast5}/Huffman_Packer.hpp          |    0
 {src => include/fast5}/cwmap.fast5_ed_len_1.inl    |    0
 {src => include/fast5}/cwmap.fast5_ed_skip_1.inl   |    0
 {src => include/fast5}/cwmap.fast5_ev_move_1.inl   |    0
 .../fast5}/cwmap.fast5_ev_rel_skip_1.inl           |    0
 {src => include/fast5}/cwmap.fast5_fq_bp_1.inl     |    0
 {src => include/fast5}/cwmap.fast5_fq_qv_1.inl     |    0
 {src => include/fast5}/cwmap.fast5_rw_1.inl        |    0
 {src => include/fast5}/fast5_version.hpp           |    0
 {src => include/fast5}/hdf5_tools.hpp              | 1449 ++++++++----
 {src => include/fast5}/logger.hpp                  |    1 +
 python/bin/f5ls                                    |    4 +-
 python/setup.py                                    |    5 +-
 src/File_Packer.hpp                                |    3 +-
 src/Makefile                                       |    5 +-
 src/f5-mod.cpp                                     |    2 +-
 src/f5dump.cpp                                     |    2 +-
 src/f5ls-full.cpp                                  |    2 +-
 src/f5ls.cpp                                       |    2 +-
 src/f5pack.cpp                                     |    3 +-
 src/hdf5-mod.cpp                                   |    2 +-
 src/huffman-decode.cpp                             |    4 +-
 src/huffman-encode.cpp                             |    4 +-
 29 files changed, 3491 insertions(+), 506 deletions(-)
 create mode 100644 Doxyfile
 rename {src => include}/fast5.hpp (99%)
 rename {src => include/fast5}/Bit_Packer.hpp (100%)
 rename {src => include/fast5}/Huffman_Packer.hpp (100%)
 rename {src => include/fast5}/cwmap.fast5_ed_len_1.inl (100%)
 rename {src => include/fast5}/cwmap.fast5_ed_skip_1.inl (100%)
 rename {src => include/fast5}/cwmap.fast5_ev_move_1.inl (100%)
 rename {src => include/fast5}/cwmap.fast5_ev_rel_skip_1.inl (100%)
 rename {src => include/fast5}/cwmap.fast5_fq_bp_1.inl (100%)
 rename {src => include/fast5}/cwmap.fast5_fq_qv_1.inl (100%)
 rename {src => include/fast5}/cwmap.fast5_rw_1.inl (100%)
 rename {src => include/fast5}/fast5_version.hpp (100%)
 rename {src => include/fast5}/hdf5_tools.hpp (55%)
 rename {src => include/fast5}/logger.hpp (99%)

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