[med-svn] [circlator] branch master updated (f62822a -> 461ff2e)

[Afif Elghraoui]

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

afif pushed a change to branch master
in repository circlator.

      from  f62822a   releasing package circlator version 1.2.1-1
       new  18c214d   Remove code to support now unnecessary second tarball
       new  cd94621   Imported Upstream version 1.3.0
       new  563d87d   Merge tag 'upstream/1.3.0'
       new  d34111f   Drop all patches - no longer required
       new  a378a3b   Remove old bio-assembly-refinement manpage stubs
       new  652f7c7   Build-depend on prodigal to run test suite
       new  461ff2e   releasing package circlator version 1.3.0-1

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                                        |   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 ++
 ...t_contigs.fasta => start_fixer_init_contigs.fa} |   0
 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 +-
 debian/README.source                               |  24 -
 debian/changelog                                   |   9 +
 debian/control                                     |   1 +
 debian/man/bio-assembly-refinement.1               |  27 -
 debian/man/contig_break_finder.1                   |   1 -
 debian/man/contig_cleaner.1                        |   1 -
 debian/man/contig_overlap_trimmer.1                |   1 -
 debian/man/pacbio_post_process.1                   |   1 -
 debian/patches/bundle-bioassemblyref.patch         |  23 -
 debian/patches/pysam-maxversion.patch              |  17 -
 debian/patches/series                              |   3 -
 debian/patches/spades-call.patch                   |  18 -
 debian/rules                                       |  11 -
 debian/watch                                       |   8 +-
 install_dependencies.sh                            |   2 +-
 setup.py                                           |   5 +-
 52 files changed, 3458 insertions(+), 245 deletions(-)
 delete mode 100644 circlator/fixstart.py
 create mode 100644 circlator/start_fixer.py
 create mode 100644 circlator/tests/data/start_fixer_find_circular_using_prodigal.ctgs.fa
 create mode 100644 circlator/tests/data/start_fixer_find_circular_using_promer.contigs.fa
 create mode 100644 circlator/tests/data/start_fixer_find_circular_using_promer.refs.fa
 copy circlator/tests/data/{assembly_test_get_contigs.fasta => start_fixer_init_contigs.fa} (100%)
 create mode 100644 circlator/tests/data/start_fixer_init_dnaA.fa
 create mode 100644 circlator/tests/data/start_fixer_init_ignore_ids
 create mode 100644 circlator/tests/data/start_fixer_max_length_from_fasta_file.fa
 create mode 100644 circlator/tests/data/start_fixer_rearrange_contigs.expect.fa
 create mode 100644 circlator/tests/data/start_fixer_rearrange_contigs.expect.log
 create mode 100644 circlator/tests/data/start_fixer_rearrange_contigs.in.fa
 create mode 100644 circlator/tests/data/start_fixer_rearrange_contigs.refs.fa
 create mode 100644 circlator/tests/data/start_fixer_run_bit_of_everything.ctg.fa
 create mode 100644 circlator/tests/data/start_fixer_run_bit_of_everything.expect.fa
 create mode 100644 circlator/tests/data/start_fixer_run_bit_of_everything.ignore
 create mode 100644 circlator/tests/data/start_fixer_run_bit_of_everything.ref.fa
 create mode 100644 circlator/tests/data/start_fixer_run_ignore_all.expect.fa
 create mode 100644 circlator/tests/data/start_fixer_run_ignore_all.fa
 create mode 100644 circlator/tests/data/start_fixer_run_ignore_all.to_ignore
 create mode 100644 circlator/tests/data/start_fixer_run_none_for_prodigal.ctg.fa
 create mode 100644 circlator/tests/data/start_fixer_run_none_for_prodigal.expect.fa
 create mode 100644 circlator/tests/data/start_fixer_run_none_for_prodigal.ref.fa
 create mode 100644 circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.in.fa
 create mode 100644 circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.fa
 create mode 100644 circlator/tests/data/start_fixer_write_fasta_plus_circularized_ends.out.ignore.fa
 create mode 100644 circlator/tests/data/start_fixer_write_renamed_contigs.fa
 create mode 100644 circlator/tests/start_fixer_test.py
 delete mode 100644 debian/README.source
 delete mode 100644 debian/man/bio-assembly-refinement.1
 delete mode 120000 debian/man/contig_break_finder.1
 delete mode 120000 debian/man/contig_cleaner.1
 delete mode 120000 debian/man/contig_overlap_trimmer.1
 delete mode 120000 debian/man/pacbio_post_process.1
 delete mode 100644 debian/patches/bundle-bioassemblyref.patch
 delete mode 100644 debian/patches/pysam-maxversion.patch
 delete mode 100644 debian/patches/spades-call.patch

-- 
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