[med-svn] [spades] branch debian/jessie-backports updated (cee9e8b -> c0f09ab)

[Afif Elghraoui]

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

afif pushed a change to branch debian/jessie-backports
in repository spades.

      from  cee9e8b   rebuild for jessie
      adds  7796bef   stop using embedded libssw,, libhat-trie and libnlopt
      adds  419b5e0   update email addresses
      adds  3739447   bump Debian version
      adds  cba6d9c   Imported Upstream version 3.8.2+dfsg
      adds  1a921ff   Merge tag 'upstream/3.8.2+dfsg'
      adds  1cb97c4   refresh patches
      adds  167726d   remove override
      adds  75b8d02   update d/changelog
      adds  3331fab   build with debug symbols
       new  a9a02cf   Merge tag 'debian/3.8.2+dfsg-1' into debian/jessie-backports
       new  12aeff3   Switch manpage building back to asciidoctor
       new  c0f09ab   Prepare backports revision

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:
 VERSION                                            |   2 +-
 changelog.html                                     |   4 +
 configs/debruijn/path_extend/pe_params.info        |   8 +-
 debian/changelog                                   |  23 +++++
 debian/control                                     |  12 ++-
 .../man_src/{dipspades.1.ronn => dipspades.1.adoc} | 101 +++++++++----------
 debian/man_src/{spades.1.ronn => spades.1.adoc}    | 103 ++++++++++----------
 .../man_src/{truspades.1.ronn => truspades.1.adoc} |  27 +++---
 debian/patches/0110_build_single_thread.patch      |   2 +-
 debian/patches/0111_use_full_config_dirs.patch     |   4 +-
 debian/patches/0112_spelling.patch                 |   2 +-
 debian/patches/0113_adjust_paths.patch             |  19 ++--
 debian/patches/0114_use_debian_provided_libs.patch |  23 ++++-
 debian/patches/0115_enable_compiler_messages.patch |   2 +-
 debian/patches/0116_stable_link_order.patch        |   2 +-
 debian/patches/0117_build_with_debug.patch         |  13 +++
 debian/patches/series                              |   1 +
 debian/rules                                       |   2 +-
 debian/spades.lintian-overrides                    |   2 -
 debian/tests/run-upstreams-tests                   |   2 +-
 ext/src/ssw/ssw.c                                  |   3 +-
 manual.html                                        |  40 ++++----
 metaspades.py                                      |   4 +-
 plasmidspades.py                                   |   4 +-
 spades.py                                          |   4 +-
 spades_init.py                                     |  29 ++++--
 src/cmake/pack.cmake                               |   4 +-
 .../algorithms/path_extend/extension_chooser.hpp   | 108 +++++++++++++--------
 .../algorithms/path_extend/loop_traverser.hpp      |  15 ++-
 .../algorithms/path_extend/overlap_analysis.hpp    |   8 +-
 .../algorithms/path_extend/path_extend_launch.hpp  |   2 +-
 src/modules/algorithms/path_extend/pe_io.hpp       |  28 +++++-
 .../simplification/complex_tip_clipper.hpp         |  11 ++-
 src/modules/paired_info/pair_info_improver.hpp     |  15 +--
 src/projects/hammer/hammer_tools.cpp               |   1 +
 src/projects/spades/distance_estimation.cpp        |   4 +-
 src/projects/spades/main.cpp                       |   3 +-
 src/spades_pipeline/spades_logic.py                |  24 +++--
 src/spades_pipeline/support.py                     |   3 +
 39 files changed, 413 insertions(+), 251 deletions(-)
 rename debian/man_src/{dipspades.1.ronn => dipspades.1.adoc} (71%)
 rename debian/man_src/{spades.1.ronn => spades.1.adoc} (71%)
 rename debian/man_src/{truspades.1.ronn => truspades.1.adoc} (61%)
 create mode 100644 debian/patches/0117_build_with_debug.patch
 delete mode 100644 debian/spades.lintian-overrides
 mode change 100644 => 100755 spades_init.py

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.git