[med-svn] [iva] 04/05: Merge tag 'upstream/1.0.4'

[Sascha Steinbiss]

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

commit 1dfad624d5512c113c1462d8d9d8fe7b2b751fad
Merge: 4cd305a 0bb6f95
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Thu Apr 28 21:37:11 2016 +0000

    Merge tag 'upstream/1.0.4'
    
    Upstream version 1.0.4

 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(-)

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