[med-svn] [roary] 02/07: Updated version 3.11.0+dfsg from 'upstream/3.11.0+dfsg'

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository roary.

commit 6a08b53e0309c676da2f93f9d84d3af5c56cc8de
Merge: f2fb3bf 622661b
Author: Sascha Steinbiss <satta at debian.org>
Date:   Wed Oct 11 10:17:34 2017 +0200

    Updated version 3.11.0+dfsg from 'upstream/3.11.0+dfsg'
    
    with Debian dir 859d58b30b47e300f98c6ebfbbaaf3fb7ee5ffad

 .travis.yml                                        | 11 ++-
 dist.ini                                           |  4 +-
 install_dependencies.sh                            | 12 ++--
 lib/Bio/Roary/CommandLine/Roary.pm                 |  2 +-
 lib/Bio/Roary/External/CheckTools.pm               |  8 +--
 lib/Bio/Roary/MergeMultifastaAlignments.pm         |  2 +-
 lib/Bio/Roary/PrepareInputFiles.pm                 | 81 +++++++++++++++-------
 lib/Bio/Roary/ReformatInputGFFs.pm                 | 72 +++++++++++++++----
 t/Bio/Roary/ReformatInputGFFs.t                    | 12 ++--
 t/data/expected_core_gene_alignment_core0.66.aln   |  2 +-
 t/data/overall_gene_presence_absence.csv           | 42 +++++------
 .../reformat_input_gffs/expected_fixed_query_2.gff | 10 +--
 12 files changed, 168 insertions(+), 90 deletions(-)

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