[med-svn] [circlator] 03/07: Merge tag 'upstream/1.3.0'
Afif Elghraoui
afif at moszumanska.debian.org
Tue Aug 16 07:07:27 UTC 2016
This is an automated email from the git hooks/post-receive script.
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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