[med-svn] [ariba] 02/06: Merge tag 'upstream/2.2.5+ds'

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository ariba.

commit 5d619c8a675ad1c915b87aa141a3fe1ecf30fbf2
Merge: 439724e d73cf5b
Author: Sascha Steinbiss <satta at debian.org>
Date:   Wed Aug 31 13:24:25 2016 +0000

    Merge tag 'upstream/2.2.5+ds'
    
    Upstream version 2.2.5+ds

 README.md                                          |   19 +-
 ariba/__init__.py                                  |    1 -
 ariba/assembly.py                                  |    3 +-
 ariba/best_seq_chooser.py                          |   98 -
 ariba/cluster.py                                   |   26 +-
 ariba/clusters.py                                  |    4 -
 ariba/ext/vcfcall_ariba.cpp                        |  245 +
 ariba/external_progs.py                            |    6 -
 ariba/faidx.py                                     |   20 +-
 ariba/mapping.py                                   |   41 +-
 ariba/ref_genes_getter.py                          |    5 +-
 ariba/report_filter.py                             |    1 -
 ariba/samtools_variants.py                         |   83 +-
 ariba/summary.py                                   |    2 +-
 ariba/summary_cluster_variant.py                   |   40 +-
 ariba/tasks/getref.py                              |    1 -
 ariba/tests/best_seq_chooser_test.py               |   69 -
 ...ls_variants_make_vcf_and_depths_files.asmbly.fa |   73 +-
 ...ariants_make_vcf_and_depths_files.asmbly.fa.fai |   10 +-
 ...samtools_variants_make_vcf_and_depths_files.bam |  Bin 21690 -> 44383 bytes
 ...s_variants_make_vcf_and_depths_files.expect.cov |    2 +
 ...ants_make_vcf_and_depths_files.expect.depths.gz |  Bin 10132 -> 5342 bytes
 ..._make_vcf_and_depths_files.expect.depths.gz.tbi |  Bin 210 -> 0 bytes
 ...s_variants_make_vcf_and_depths_files.expect.vcf |   47 +-
 ...variants_make_vcf_and_depths_files.for_reads.fa |   80 +
 ...s_variants_make_vcf_and_depths_files.reads_1.fq | 5704 ++++++++++++++++++++
 ...s_variants_make_vcf_and_depths_files.reads_2.fq | 5704 ++++++++++++++++++++
 .../samtools_variants_test_total_depth_per_contig  |    9 +-
 ariba/tests/data/summary_test_whole_run.in.1.tsv   |   16 +
 ariba/tests/data/summary_test_whole_run.in.2.tsv   |    7 +
 ariba/tests/data/summary_test_whole_run.out.csv    |    3 +
 ariba/tests/faidx_test.py                          |    2 +-
 ariba/tests/mapping_test.py                        |    3 -
 ariba/tests/samtools_variants_test.py              |   15 +-
 ariba/tests/summary_cluster_variant_test.py        |   45 +-
 ariba/tests/summary_test.py                        |   28 +
 install_dependencies.sh                            |   25 -
 scripts/ariba                                      |    1 -
 setup.py                                           |   10 +-
 39 files changed, 11986 insertions(+), 462 deletions(-)

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