[med-svn] [roary] branch master updated (f2fb3bf -> b250f7d)

[Sascha Steinbiss]

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

satta pushed a change to branch master
in repository roary.

      from  f2fb3bf   new upstream release
       new  622661b   New upstream version 3.11.0+dfsg
       new  6a08b53   Updated version 3.11.0+dfsg from 'upstream/3.11.0+dfsg'
       new  fc7ee5d   new upstream release
       new  726fa48   bump Standards-Version
       new  b2e9e78   re-introduce @Basic type
       new  8008d0f   add missing dep on libdigest-md5-file-perl
       new  b250f7d   remove obsolete Testsuite: entry

The 7 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:
 .travis.yml                                        | 11 ++-
 debian/changelog                                   |  9 +++
 debian/control                                     |  4 +-
 debian/patches/series                              |  1 +
 debian/patches/use-dz-starter.patch                | 13 ++++
 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 +--
 16 files changed, 193 insertions(+), 92 deletions(-)
 create mode 100644 debian/patches/use-dz-starter.patch

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