[med-svn] [ariba] 02/06: Merge tag 'upstream/2.6.0+ds'

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository ariba.

commit 9160b2b5adbf40f4f70c132fee1511fe32edfa63
Merge: 69ca72b 4cf37d7
Author: Sascha Steinbiss <satta at debian.org>
Date:   Wed Dec 21 10:38:45 2016 +0000

    Merge tag 'upstream/2.6.0+ds'
    
    Upstream version 2.6.0+ds

 README.md                                          |    2 +-
 ariba/__init__.py                                  |    4 +
 ariba/clusters.py                                  |   17 +-
 ariba/ext/vcfcall_ariba.cpp                        |   82 +-
 ariba/mlst_profile.py                              |   57 +
 ariba/mlst_reporter.py                             |  113 +
 ariba/pubmlst_getter.py                            |  114 +
 ariba/pubmlst_ref_preparer.py                      |  101 +
 ariba/report.py                                    |    1 -
 ariba/samtools_variants.py                         |    4 +-
 ariba/tasks/__init__.py                            |    2 +
 ariba/tasks/pubmlstget.py                          |   12 +
 ariba/tasks/pubmlstspecies.py                      |    8 +
 ariba/tests/clusters_test.py                       |   20 +
 ...usters_test_write_mlst_reports.ariba.report.tsv |    3 +
 ...usters_test_write_mlst_reports.mlst_profile.tsv |    5 +
 ...lusters_test_write_mlst_reports.out.details.tsv |    3 +
 .../data/clusters_test_write_mlst_reports.out.tsv  |    2 +
 .../tests/data/mlst_profile_test.init.profile.tsv  |    4 +
 ariba/tests/data/mlst_profile_test.profile.tsv     |    3 +
 ...mlst_reporter.all_present_perfect.report.in.tsv |    3 +
 ...rter.all_present_perfect.report.out.details.tsv |    3 +
 ...lst_reporter.all_present_perfect.report.out.tsv |    2 +
 ariba/tests/data/mlst_reporter.het_snp.in.tsv      |    3 +
 .../data/mlst_reporter.het_snp.out.details.tsv     |    3 +
 ariba/tests/data/mlst_reporter.het_snp.out.tsv     |    2 +
 ariba/tests/data/mlst_reporter.het_snps.in.tsv     |    4 +
 .../data/mlst_reporter.het_snps.out.details.tsv    |    3 +
 ariba/tests/data/mlst_reporter.het_snps.out.tsv    |    2 +
 .../tests/data/mlst_reporter.new_st.report.in.tsv  |    3 +
 .../mlst_reporter.new_st.report.out.details.tsv    |    3 +
 .../tests/data/mlst_reporter.new_st.report.out.tsv |    2 +
 .../data/mlst_reporter.one_gene_missing.in.tsv     |    2 +
 .../mlst_reporter.one_gene_missing.out.details.tsv |    3 +
 .../data/mlst_reporter.one_gene_missing.out.tsv    |    2 +
 ariba/tests/data/mlst_reporter.profile.in.tsv      |    5 +
 ariba/tests/data/pubmlst_getter.dbases.xml         |  101 +
 ...ef_prepare.test_load_fa_and_clusters.expect.tsv |    2 +
 .../gene1.tfa                                      |    4 +
 .../gene2.tfa                                      |    4 +
 .../profile.txt                                    |    4 +
 ariba/tests/data/pubmlst_rename_seqs.expected.fa   |    6 +
 ariba/tests/data/pubmlst_rename_seqs.in.fa         |    6 +
 ...ls_variants_make_vcf_and_depths_files.asmbly.fa |   14 +-
 ...ariants_make_vcf_and_depths_files.asmbly.fa.fai |    4 +-
 ...samtools_variants_make_vcf_and_depths_files.bam |  Bin 44383 -> 22642 bytes
 ...s_variants_make_vcf_and_depths_files.expect.cov |    4 +-
 ...ants_make_vcf_and_depths_files.expect.depths.gz |  Bin 5342 -> 4786 bytes
 ...s_variants_make_vcf_and_depths_files.expect.vcf |    8 +-
 ...variants_make_vcf_and_depths_files.for_reads.fa |   80 +
 ...s_variants_make_vcf_and_depths_files.reads_1.fq | 5698 ++++++++++----------
 ...s_variants_make_vcf_and_depths_files.reads_2.fq | 5694 ++++++++++---------
 ariba/tests/mlst_profile_test.py                   |   47 +
 ariba/tests/mlst_reporter_test.py                  |   93 +
 ariba/tests/pubmlst_getter_test.py                 |   51 +
 ariba/tests/pubmlst_ref_preparer_test.py           |   58 +
 scripts/ariba                                      |   23 +
 setup.py                                           |    2 +-
 58 files changed, 6767 insertions(+), 5738 deletions(-)

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