[med-svn] [iva] branch master updated (16708db -> 8bb71e3)

[Sascha Steinbiss]

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

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

      from  16708db   use trimmomatic in autopkgtest
       new  7f93763   version bump
       new  5fd9425   Imported Upstream version 1.0.5
       new  cdc2a36   Merge tag 'upstream/1.0.5'
       new  d1436c4   drop patches applied by upstream
       new  aaab867   make scripts executable
       new  8bb71e3   dch -r

The 6 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:
 debian/changelog                                   |  4 ++--
 debian/patches/adjust_required_pysam_version.patch |  2 +-
 debian/patches/series                              |  2 --
 debian/rules                                       |  1 +
 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 ++++++++++++-
 50 files changed, 669 insertions(+), 35 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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