[med-svn] [spades] 01/03: Merge tag 'debian/3.8.2+dfsg-1' into debian/jessie-backports

[Afif Elghraoui]

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

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

commit a9a02cf3cc2b63fde8ddf3e91ef2988cc710989f
Merge: cee9e8b 3331fab
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sun Jul 17 20:36:51 2016 -0700

    Merge tag 'debian/3.8.2+dfsg-1' into debian/jessie-backports
    
    spades Debian release 3.8.2+dfsg-1

 VERSION                                            |   2 +-
 changelog.html                                     |   4 +
 configs/debruijn/path_extend/pe_params.info        |   8 +-
 debian/changelog                                   |  16 +++
 debian/control                                     |  10 +-
 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/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 +
 35 files changed, 284 insertions(+), 138 deletions(-)

diff --cc debian/changelog
index eac8676,87c533a..fedb4ce
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,19 +1,25 @@@
+ spades (3.8.2+dfsg-1) unstable; urgency=medium
+ 
+   * New upstream release.
+   * Adapt patches for new upstream code.
+   * Remove unused override.
+   * Build with debug symbols.
+ 
+  -- Sascha Steinbiss <satta at debian.org>  Mon, 11 Jul 2016 08:39:53 +0000
+ 
+ spades (3.8.1+dfsg-2) unstable; urgency=medium
+ 
+   * Stop using embedded libnlopt, libssw and libhat-trie.
+   * Update email addresses.
+ 
+  -- Sascha Steinbiss <satta at debian.org>  Sat, 02 Jul 2016 17:45:37 +0000
+ 
 +spades (3.8.1+dfsg-1~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports.
 +
 + -- Sascha Steinbiss <sascha at steinbiss.name>  Mon, 13 Jun 2016 09:52:56 +0000
 +
  spades (3.8.1+dfsg-1) unstable; urgency=medium
  
    * New upstream release.
diff --cc debian/control
index 0266114,e02d81e..f4763fb
--- a/debian/control
+++ b/debian/control
@@@ -15,10 -15,13 +15,13 @@@ Build-Depends: debhelper (>= 9)
                 libbam-dev,
                 libbamtools-dev,
                 libjemalloc-dev,
+                libhat-trie-dev,
                 libhts-dev,
+                libnlopt-dev,
+                libssw-dev,
                 python-yaml,
                 python-joblib,
 -               asciidoctor (>= 1.5.3),
 +               ruby-ronn,
                 bwa,
                 lynx
  Standards-Version: 3.9.8

-- 
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