[med-svn] [iva] 02/04: Merge tag 'upstream/1.0.0'

[Sascha Steinbiss]

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

commit abbcc4077fd840df65b485b2b02e447311871dbc
Merge: 9b2bdfb 39b4dbf
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Mon Aug 24 21:54:34 2015 +0000

    Merge tag 'upstream/1.0.0'
    
    Upstream version 1.0.0

 README.md                                          | 138 +----
 iva/__init__.py                                    |   1 +
 iva/assembly.py                                    |  53 +-
 iva/common.py                                      |   2 +-
 iva/contig_trim.py                                 |  10 +-
 iva/edge.py                                        |   2 +-
 iva/egg_extract.py                                 |  77 +++
 iva/external_progs.py                              |   9 +-
 iva/gage/getCorrectnessStats.sh                    |   2 +-
 iva/gage/getMummerStats.sh                         |  30 +-
 iva/graph.py                                       |   2 +-
 iva/kcount.py                                      |  52 +-
 iva/kraken.py                                      |  40 +-
 iva/mapping.py                                     |  50 +-
 iva/mummer.py                                      |  14 +-
 iva/qc.py                                          | 188 +++---
 iva/qc_external.py                                 |  78 +--
 iva/seed.py                                        |   8 +-
 iva/seed_processor.py                              |  16 +-
 iva/tests/assembly_test.py                         |   2 +-
 iva/tests/contig_test.py                           |   2 +-
 iva/tests/data/contig_trim_test_contigs.fa         |   2 +
 iva/tests/data/egg_extract_test_dir.zip            | Bin 0 -> 1230 bytes
 iva/tests/data/egg_extract_test_dir/.zip           | Bin 0 -> 1322 bytes
 iva/tests/data/egg_extract_test_dir/file1          |   0
 iva/tests/data/egg_extract_test_dir/iva/gage/gage1 |   2 +
 iva/tests/data/egg_extract_test_dir/iva/gage/gage2 |   0
 iva/tests/data/egg_extract_test_dir/iva/ratt/ratt1 |   0
 iva/tests/data/egg_extract_test_dir/iva/ratt/ratt2 |   0
 iva/tests/data/qc_external_test_run_gage.out       |  55 ++
 iva/tests/data/qc_external_test_run_gage.ref.fa    |  51 ++
 iva/tests/data/qc_external_test_run_gage.scaffs.fa |  53 ++
 .../data/qc_external_test_run_ratt.assembly.fa     | 155 +++++
 .../data/qc_external_test_run_ratt.embl/hiv-1.embl | 645 +++++++++++++++++++++
 iva/tests/edge_test.py                             |   2 +-
 iva/tests/egg_extract_test.py                      | 105 ++++
 iva/tests/graph_test.py                            |   2 +-
 iva/tests/mapping_test.py                          |   6 +-
 iva/tests/mummer_test.py                           |   6 +-
 iva/tests/qc_external_test.py                      |  33 ++
 iva/tests/qc_test.py                               | 148 ++---
 iva/tests/seed_processor_test.py                   |   4 +-
 iva/tests/seed_test.py                             |  26 +-
 scripts/iva                                        |  54 +-
 scripts/iva_qc                                     |   2 +-
 setup.py                                           |  48 +-
 46 files changed, 1659 insertions(+), 516 deletions(-)

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