[med-svn] [spades] branch master updated (3739447 -> 3331fab)

[Sascha Steinbiss]

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satta pushed a change to branch master
in repository spades.

      from  3739447   bump Debian version
       new  cba6d9c   Imported Upstream version 3.8.2+dfsg
       new  1a921ff   Merge tag 'upstream/3.8.2+dfsg'
       new  1cb97c4   refresh patches
       new  167726d   remove override
       new  75b8d02   update d/changelog
       new  3331fab   build with debug symbols

The 6 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                                   |   9 ++
 debian/patches/0111_use_full_config_dirs.patch     |   2 +-
 debian/patches/0113_adjust_paths.patch             |  17 +++-
 debian/patches/0117_build_with_debug.patch         |  13 +++
 debian/patches/series                              |   1 +
 debian/spades.lintian-overrides                    |   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 +
 28 files changed, 243 insertions(+), 125 deletions(-)
 create mode 100644 debian/patches/0117_build_with_debug.patch
 delete mode 100644 debian/spades.lintian-overrides
 mode change 100644 => 100755 spades_init.py

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