[med-svn] [iva] 03/06: Merge tag 'upstream/1.0.5'

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository iva.

commit cdc2a36d1e370ae898792185d6e2a295ec78f314
Merge: 7f93763 5fd9425
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Thu May 5 09:17:44 2016 +0000

    Merge tag 'upstream/1.0.5'
    
    Upstream version 1.0.5

 iva/__init__.py                  | 14 ++++++++++++++
 iva/assembly.py                  | 14 ++++++++++++++
 iva/common.py                    | 16 +++++++++++++++-
 iva/contig.py                    | 14 ++++++++++++++
 iva/contig_trim.py               | 14 ++++++++++++++
 iva/edge.py                      | 14 ++++++++++++++
 iva/egg_extract.py               | 14 ++++++++++++++
 iva/external_progs.py            | 18 ++++++++++++++++--
 iva/graph.py                     | 14 ++++++++++++++
 iva/kcount.py                    | 14 ++++++++++++++
 iva/kmers.py                     | 14 ++++++++++++++
 iva/kraken.py                    | 14 ++++++++++++++
 iva/mapping.py                   | 20 +++++++++++++++++++-
 iva/mummer.py                    | 14 ++++++++++++++
 iva/qc.py                        | 14 ++++++++++++++
 iva/qc_external.py               | 28 ++++++++++++++++++++++------
 iva/ratt/embl2gff.pl             | 14 ++++++++++++++
 iva/ratt/genbank2embl.pl         | 15 +++++++++++++++
 iva/ratt/main.ratt.pl            | 21 ++++++++++++---------
 iva/ratt/ratt_correction.pm      | 19 ++++++++++++++-----
 iva/ratt/start.ratt.sh           | 15 ++++++++++++++-
 iva/read_trim.py                 | 14 ++++++++++++++
 iva/seed.py                      | 14 ++++++++++++++
 iva/seed_processor.py            | 14 ++++++++++++++
 iva/test_data_runner.py          | 16 +++++++++++++++-
 iva/tests/assembly_test.py       | 14 ++++++++++++++
 iva/tests/contig_test.py         | 14 ++++++++++++++
 iva/tests/contig_trim_test.py    | 14 ++++++++++++++
 iva/tests/edge_test.py           | 14 ++++++++++++++
 iva/tests/egg_extract_test.py    | 14 ++++++++++++++
 iva/tests/external_progs_test.py | 14 ++++++++++++++
 iva/tests/graph_test.py          | 14 ++++++++++++++
 iva/tests/kcount_test.py         | 14 ++++++++++++++
 iva/tests/kmers_test.py          | 14 ++++++++++++++
 iva/tests/kraken_test.py         | 14 ++++++++++++++
 iva/tests/mapping_test.py        | 14 ++++++++++++++
 iva/tests/mummer_test.py         | 14 ++++++++++++++
 iva/tests/qc_external_test.py    | 14 ++++++++++++++
 iva/tests/qc_test.py             | 14 ++++++++++++++
 iva/tests/read_trim_test.py      | 14 ++++++++++++++
 iva/tests/seed_processor_test.py | 14 ++++++++++++++
 iva/tests/seed_test.py           | 14 ++++++++++++++
 scripts/iva                      | 20 +++++++++++++++++---
 scripts/iva_qc                   | 14 ++++++++++++++
 scripts/iva_qc_make_db           | 14 ++++++++++++++
 setup.py                         | 17 ++++++++++++++++-
 46 files changed, 665 insertions(+), 30 deletions(-)

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