[med-svn] [spades] 02/06: Merge tag 'upstream/3.8.2+dfsg'

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository spades.

commit 1a921ff7ad446f01f7cfbe2172e0cee6ad4e4268
Merge: 3739447 cba6d9c
Author: Sascha Steinbiss <satta at debian.org>
Date:   Mon Jul 11 08:36:28 2016 +0000

    Merge tag 'upstream/3.8.2+dfsg'
    
    Upstream version 3.8.2+dfsg

 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(-)

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