[med-svn] [circlator] 03/07: Merge tag 'upstream/1.3.0'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository circlator.

commit 563d87d164dae4de6243ec836433011c89277378
Merge: 18c214d cd94621
Author: Afif Elghraoui <afif at debian.org>
Date:   Mon Aug 15 20:54:34 2016 -0700

    Merge tag 'upstream/1.3.0'
    
    Upstream version 1.3.0

 .travis.yml                                        |   4 -
 circlator/__init__.py                              |   2 +-
 circlator/external_progs.py                        |  45 +-
 circlator/fixstart.py                              |  55 --
 circlator/program.py                               |  55 +-
 circlator/start_fixer.py                           | 337 +++++++++
 circlator/tasks/all.py                             |   5 +-
 circlator/tasks/fixstart.py                        |   6 +-
 circlator/tasks/progcheck.py                       |   6 +-
 ...tart_fixer_find_circular_using_prodigal.ctgs.fa | 109 +++
 ...art_fixer_find_circular_using_promer.contigs.fa | 168 +++++
 .../start_fixer_find_circular_using_promer.refs.fa |  75 ++
 circlator/tests/data/start_fixer_init_contigs.fa   |   4 +
 circlator/tests/data/start_fixer_init_dnaA.fa      |   2 +
 circlator/tests/data/start_fixer_init_ignore_ids   |   2 +
 .../data/start_fixer_max_length_from_fasta_file.fa |   6 +
 .../data/start_fixer_rearrange_contigs.expect.fa   | 776 +++++++++++++++++++++
 .../data/start_fixer_rearrange_contigs.expect.log  |   8 +
 .../tests/data/start_fixer_rearrange_contigs.in.fa | 776 +++++++++++++++++++++
 .../data/start_fixer_rearrange_contigs.refs.fa     |  50 ++
 .../data/start_fixer_run_bit_of_everything.ctg.fa  | 282 ++++++++
 .../start_fixer_run_bit_of_everything.expect.fa    | 282 ++++++++
 .../data/start_fixer_run_bit_of_everything.ignore  |   1 +
 .../data/start_fixer_run_bit_of_everything.ref.fa  |  25 +
 .../data/start_fixer_run_ignore_all.expect.fa      |   2 +
 circlator/tests/data/start_fixer_run_ignore_all.fa |   2 +
 .../data/start_fixer_run_ignore_all.to_ignore      |   1 +
 .../data/start_fixer_run_none_for_prodigal.ctg.fa  |  91 +++
 .../start_fixer_run_none_for_prodigal.expect.fa    |  91 +++
 .../data/start_fixer_run_none_for_prodigal.ref.fa  |  25 +
 ..._fixer_write_fasta_plus_circularized_ends.in.fa |   8 +
 ...fixer_write_fasta_plus_circularized_ends.out.fa |  12 +
 ...rite_fasta_plus_circularized_ends.out.ignore.fa |   6 +
 .../data/start_fixer_write_renamed_contigs.fa      |   4 +
 circlator/tests/start_fixer_test.py                | 225 ++++++
 circlator/versions.py                              |   7 +-
 install_dependencies.sh                            |   2 +-
 setup.py                                           |   5 +-
 38 files changed, 3451 insertions(+), 111 deletions(-)

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