[med-svn] [spades] branch upstream updated (bc265dc -> cba6d9c)

[Sascha Steinbiss]

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satta pushed a change to branch upstream
in repository spades.

      from  bc265dc   Imported Upstream version 3.8.1+dfsg
       new  cba6d9c   Imported Upstream version 3.8.2+dfsg

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
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Summary of changes:
 VERSION                                            |   2 +-
 changelog.html                                     |   4 +
 configs/debruijn/path_extend/pe_params.info        |   8 +-
 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 +
 22 files changed, 207 insertions(+), 117 deletions(-)
 mode change 100644 => 100755 spades_init.py

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