[med-svn] [spades] branch upstream updated (bc265dc -> cba6d9c)
Sascha Steinbiss
satta at debian.org
Mon Jul 11 10:02:07 UTC 2016
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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
been added to this reference.
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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