[med-svn] [circlator] branch master updated (92736a6 -> 90dbc22)

[Sascha Steinbiss]

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satta pushed a change to branch master
in repository circlator.

      from  92736a6   new upstream release
       new  e6369ca   New upstream version 1.5.1
       new  db03f09   Merge tag 'upstream/1.5.1'
       new  e25e6d8   new upstream release
       new  90dbc22   support Canu as alternative assembler

The 4 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:
 AUTHORS                                            |  2 +
 circlator/assemble.py                              | 69 +++++++++++++++--
 circlator/assembly.py                              | 90 +++++++++++++++-------
 circlator/bamfilter.py                             | 32 +++++++-
 circlator/common.py                                |  3 +
 circlator/external_progs.py                        | 17 +++-
 circlator/merge.py                                 | 25 ++++--
 circlator/tasks/all.py                             | 17 +++-
 circlator/tasks/assemble.py                        |  6 +-
 circlator/tasks/bam2reads.py                       |  2 +
 circlator/tasks/merge.py                           |  8 ++
 circlator/tests/assemble_test.py                   | 33 ++++++++
 circlator/tests/assembly_test.py                   | 30 +++++---
 .../assemble_test_rename_canu_contigs.expect.fa    |  8 ++
 .../data/assemble_test_rename_canu_contigs.in.fa   |  8 ++
 .../assembly_test_circular_contigs_from_canu.gfa   | 14 ++++
 circlator/versions.py                              |  4 +-
 debian/changelog                                   |  9 +++
 debian/control                                     |  4 +-
 install_dependencies.sh                            | 10 +++
 setup.py                                           |  4 +-
 21 files changed, 326 insertions(+), 69 deletions(-)
 create mode 100644 circlator/tests/data/assemble_test_rename_canu_contigs.expect.fa
 create mode 100644 circlator/tests/data/assemble_test_rename_canu_contigs.in.fa
 create mode 100644 circlator/tests/data/assembly_test_circular_contigs_from_canu.gfa

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