[med-svn] [fastaq] branch master updated (d5825d3 -> 3cf4270)

[Sascha Steinbiss]

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sascha-guest pushed a change to branch master
in repository fastaq.

      from  d5825d3   Remove empty template
       new  08dda22   Imported Upstream version 3.6.1
       new  f9e43d4   Merge tag 'upstream/3.6.1'
       new  eab28ec   update upstream version
       new  1e6837d   change man page creation
       new  3cf4270   adjust d/changelog

The 5 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
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Summary of changes:
 debian/changelog                                   |   6 +-
 debian/control                                     | 142 +--------------------
 debian/make_man                                    |  16 +++
 debian/rules                                       |   5 +-
 debian/usage_to_man                                | 142 ---------------------
 pyfastaq/common.py                                 |   2 +-
 pyfastaq/genetic_codes.py                          |  31 +++++
 pyfastaq/intervals.py                              |   7 +
 pyfastaq/runners/to_fasta.py                       |   4 +-
 pyfastaq/runners/to_orfs_gff.py                    |   2 +-
 pyfastaq/sequences.py                              |  24 +++-
 pyfastaq/tasks.py                                  |  60 ++++++++-
 ...o_fasta.strip_after_whitespace_non_unique.in.fa |   6 +
 ..._fasta.strip_after_whitespace_non_unique.out.fa |   6 +
 ...st.to_fasta.strip_after_whitespace_unique.in.fa |   6 +
 ...t.to_fasta.strip_after_whitespace_unique.out.fa |   6 +
 pyfastaq/tests/data/tasks_test_to_fastg.fasta      |   4 +
 pyfastaq/tests/data/tasks_test_to_fastg.fastg      |   8 ++
 ....ids => tasks_test_to_fastg.ids_to_circularise} |   1 -
 pyfastaq/tests/intervals_test.py                   |  10 ++
 pyfastaq/tests/sequences_test.py                   |  30 +++++
 pyfastaq/tests/tasks_test.py                       |  45 +++++++
 setup.py                                           |  13 +-
 23 files changed, 269 insertions(+), 307 deletions(-)
 create mode 100644 debian/make_man
 delete mode 100755 debian/usage_to_man
 create mode 100644 pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_non_unique.in.fa
 create mode 100644 pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_non_unique.out.fa
 create mode 100644 pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_unique.in.fa
 create mode 100644 pyfastaq/tests/data/sequences_test.to_fasta.strip_after_whitespace_unique.out.fa
 create mode 100644 pyfastaq/tests/data/tasks_test_to_fastg.fasta
 create mode 100644 pyfastaq/tests/data/tasks_test_to_fastg.fastg
 copy pyfastaq/tests/data/{sequences_test_filter_by_ids_file.fa.ids => tasks_test_to_fastg.ids_to_circularise} (50%)

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