[med-svn] [ariba] branch upstream updated (713f261 -> f56815e)

[Sascha Steinbiss]

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satta pushed a change to branch upstream
in repository ariba.

      from  713f261   New upstream version 2.5.1+ds
       new  4cf37d7   New upstream version 2.6.0+ds
       new  f56815e   New upstream version 2.6.1+ds

The 2 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                                          |    2 +-
 ariba/__init__.py                                  |    4 +
 ariba/clusters.py                                  |   17 +-
 ariba/ext/vcfcall_ariba.cpp                        |   82 +-
 ariba/mlst_profile.py                              |   56 +
 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 +
 ...sters_test_write_mlst_reports.ariba.report.tsv} |    4 +-
 ...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 +
 ...le_test.init_multiple_extra_columns.profile.tsv |    3 +
 ariba/tests/data/mlst_profile_test.profile.tsv     |    3 +
 ...lst_reporter.all_present_perfect.report.in.tsv} |    4 +-
 ...rter.all_present_perfect.report.out.details.tsv |    3 +
 ...lst_reporter.all_present_perfect.report.out.tsv |    2 +
 ...ite_report.tsv => mlst_reporter.het_snp.in.tsv} |    4 +-
 .../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 +
 ...port.tsv => mlst_reporter.new_st.report.in.tsv} |    4 +-
 .../mlst_reporter.new_st.report.out.details.tsv    |    3 +
 .../tests/data/mlst_reporter.new_st.report.out.tsv |    2 +
 ...t.tsv => mlst_reporter.one_gene_missing.in.tsv} |    3 +-
 .../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                   |   60 +
 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 +-
 59 files changed, 6777 insertions(+), 5748 deletions(-)
 create mode 100644 ariba/mlst_profile.py
 create mode 100644 ariba/mlst_reporter.py
 create mode 100644 ariba/pubmlst_getter.py
 create mode 100644 ariba/pubmlst_ref_preparer.py
 create mode 100644 ariba/tasks/pubmlstget.py
 create mode 100644 ariba/tasks/pubmlstspecies.py
 copy ariba/tests/data/{clusters_test_write_report.tsv => clusters_test_write_mlst_reports.ariba.report.tsv} (59%)
 create mode 100644 ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv
 create mode 100644 ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv
 create mode 100644 ariba/tests/data/clusters_test_write_mlst_reports.out.tsv
 create mode 100644 ariba/tests/data/mlst_profile_test.init.profile.tsv
 create mode 100644 ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv
 create mode 100644 ariba/tests/data/mlst_profile_test.profile.tsv
 copy ariba/tests/data/{clusters_test_write_report.tsv => mlst_reporter.all_present_perfect.report.in.tsv} (59%)
 create mode 100644 ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv
 create mode 100644 ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv
 copy ariba/tests/data/{clusters_test_write_report.tsv => mlst_reporter.het_snp.in.tsv} (57%)
 create mode 100644 ariba/tests/data/mlst_reporter.het_snp.out.details.tsv
 create mode 100644 ariba/tests/data/mlst_reporter.het_snp.out.tsv
 create mode 100644 ariba/tests/data/mlst_reporter.het_snps.in.tsv
 create mode 100644 ariba/tests/data/mlst_reporter.het_snps.out.details.tsv
 create mode 100644 ariba/tests/data/mlst_reporter.het_snps.out.tsv
 copy ariba/tests/data/{clusters_test_write_report.tsv => mlst_reporter.new_st.report.in.tsv} (58%)
 create mode 100644 ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv
 create mode 100644 ariba/tests/data/mlst_reporter.new_st.report.out.tsv
 copy ariba/tests/data/{clusters_test_write_report.tsv => mlst_reporter.one_gene_missing.in.tsv} (74%)
 create mode 100644 ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv
 create mode 100644 ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv
 create mode 100644 ariba/tests/data/mlst_reporter.profile.in.tsv
 create mode 100644 ariba/tests/data/pubmlst_getter.dbases.xml
 create mode 100644 ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv
 create mode 100644 ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa
 create mode 100644 ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa
 create mode 100644 ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt
 create mode 100644 ariba/tests/data/pubmlst_rename_seqs.expected.fa
 create mode 100644 ariba/tests/data/pubmlst_rename_seqs.in.fa
 create mode 100644 ariba/tests/mlst_profile_test.py
 create mode 100644 ariba/tests/mlst_reporter_test.py
 create mode 100644 ariba/tests/pubmlst_getter_test.py
 create mode 100644 ariba/tests/pubmlst_ref_preparer_test.py

-- 
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