[med-svn] [iva] branch upstream updated (b7cc516 -> 39b4dbf)

[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  b7cc516   Imported Upstream version 0.10.1
       new  39b4dbf   Imported Upstream version 1.0.0

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:
 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
 .../1.embl => egg_extract_test_dir/file1}          |   0
 iva/tests/data/egg_extract_test_dir/iva/gage/gage1 |   2 +
 .../1.embl => egg_extract_test_dir/iva/gage/gage2} |   0
 .../1.embl => egg_extract_test_dir/iva/ratt/ratt1} |   0
 .../1.embl => 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(-)
 create mode 100644 iva/egg_extract.py
 mode change 100644 => 100755 iva/gage/getCorrectnessStats.sh
 create mode 100644 iva/tests/data/egg_extract_test_dir.zip
 create mode 100644 iva/tests/data/egg_extract_test_dir/.zip
 copy iva/tests/data/{kraken_test.db/EMBL/Human_immunodeficiency_virus_1/1.embl => egg_extract_test_dir/file1} (100%)
 create mode 100644 iva/tests/data/egg_extract_test_dir/iva/gage/gage1
 copy iva/tests/data/{kraken_test.db/EMBL/Human_immunodeficiency_virus_1/1.embl => egg_extract_test_dir/iva/gage/gage2} (100%)
 copy iva/tests/data/{kraken_test.db/EMBL/Human_immunodeficiency_virus_1/1.embl => egg_extract_test_dir/iva/ratt/ratt1} (100%)
 copy iva/tests/data/{kraken_test.db/EMBL/Human_immunodeficiency_virus_1/1.embl => egg_extract_test_dir/iva/ratt/ratt2} (100%)
 create mode 100644 iva/tests/data/qc_external_test_run_gage.out
 create mode 100644 iva/tests/data/qc_external_test_run_gage.ref.fa
 create mode 100644 iva/tests/data/qc_external_test_run_gage.scaffs.fa
 create mode 100644 iva/tests/data/qc_external_test_run_ratt.assembly.fa
 create mode 100644 iva/tests/data/qc_external_test_run_ratt.embl/hiv-1.embl
 create mode 100644 iva/tests/egg_extract_test.py
 create mode 100644 iva/tests/qc_external_test.py

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