[med-svn] [circlator] branch upstream updated (2224d66 -> e6369ca)

[Sascha Steinbiss]

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satta pushed a change to branch upstream
in repository circlator.

      from  2224d66   New upstream version 1.4.1
       new  e6369ca   New upstream version 1.5.1

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:
 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 +-
 install_dependencies.sh                            | 10 +++
 setup.py                                           |  4 +-
 19 files changed, 314 insertions(+), 68 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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