[med-svn] [iva] branch upstream updated (0bb6f95 -> 5fd9425)

[Sascha Steinbiss]

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

sascha-guest pushed a change to branch upstream
in repository iva.

      from  0bb6f95   Imported Upstream version 1.0.4
       new  5fd9425   Imported Upstream version 1.0.5

The 1 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:
 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(-)
 mode change 100755 => 100644 scripts/iva
 mode change 100755 => 100644 scripts/iva_qc
 mode change 100755 => 100644 scripts/iva_qc_make_db

-- 
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