[med-svn] [iva] branch upstream updated (39b4dbf -> 0bb6f95)

[Sascha Steinbiss]

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

      from  39b4dbf   Imported Upstream version 1.0.0
       new  0bb6f95   Imported Upstream version 1.0.4

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                                    |   1 +
 iva/assembly.py                                    |   5 +-
 iva/common.py                                      |   2 +-
 iva/external_progs.py                              |   8 +
 iva/gage/GetFastaStats$ContigAt.class              | Bin 489 -> 0 bytes
 iva/gage/GetFastaStats.class                       | Bin 9674 -> 0 bytes
 iva/gage/SizeFasta.class                           | Bin 3241 -> 0 bytes
 iva/gage/SplitFastaByLetter.class                  | Bin 2497 -> 0 bytes
 iva/gage/Utils$Pair.class                          | Bin 621 -> 0 bytes
 iva/gage/Utils$ToProtein.class                     | Bin 4565 -> 0 bytes
 iva/gage/Utils$Translate.class                     | Bin 1226 -> 0 bytes
 iva/gage/Utils.class                               | Bin 5321 -> 0 bytes
 iva/gage/getScaffoldStats$1.class                  | Bin 199 -> 0 bytes
 iva/gage/getScaffoldStats$Scaffold.class           | Bin 1232 -> 0 bytes
 iva/gage/getScaffoldStats.class                    | Bin 12187 -> 0 bytes
 iva/kcount.py                                      |  16 +-
 iva/kraken.py                                      |  21 +--
 iva/seed.py                                        |   7 +-
 iva/seed_processor.py                              |   7 +-
 iva/test_data_runner.py                            |  50 ++++++
 iva/test_run_data/hiv_pcr_primers.fa               |  36 +++++
 iva/test_run_data/iva_contigs_no_trimmomatic.fasta | 167 +++++++++++++++++++++
 .../iva_contigs_with_trimmomatic.fasta             | 152 +++++++++++++++++++
 iva/test_run_data/reads_1.fq.gz                    | Bin 0 -> 3813239 bytes
 iva/test_run_data/reads_2.fq.gz                    | Bin 0 -> 4661713 bytes
 iva/test_run_data/reference.fasta                  | 152 +++++++++++++++++++
 iva/tests/kcount_test.py                           |   8 +
 scripts/iva                                        |  19 +++
 setup.py                                           |   8 +-
 29 files changed, 629 insertions(+), 30 deletions(-)
 delete mode 100644 iva/gage/GetFastaStats$ContigAt.class
 delete mode 100644 iva/gage/GetFastaStats.class
 delete mode 100644 iva/gage/SizeFasta.class
 delete mode 100644 iva/gage/SplitFastaByLetter.class
 delete mode 100644 iva/gage/Utils$Pair.class
 delete mode 100644 iva/gage/Utils$ToProtein.class
 delete mode 100644 iva/gage/Utils$Translate.class
 delete mode 100644 iva/gage/Utils.class
 delete mode 100644 iva/gage/getScaffoldStats$1.class
 delete mode 100644 iva/gage/getScaffoldStats$Scaffold.class
 delete mode 100644 iva/gage/getScaffoldStats.class
 create mode 100644 iva/test_data_runner.py
 create mode 100644 iva/test_run_data/hiv_pcr_primers.fa
 create mode 100644 iva/test_run_data/iva_contigs_no_trimmomatic.fasta
 create mode 100644 iva/test_run_data/iva_contigs_with_trimmomatic.fasta
 create mode 100644 iva/test_run_data/reads_1.fq.gz
 create mode 100644 iva/test_run_data/reads_2.fq.gz
 create mode 100644 iva/test_run_data/reference.fasta

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