[med-svn] [ariba] 03/06: Merge tag 'upstream/2.1.0+ds'

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository ariba.

commit 8e6ac7fec8b7d8643a5e5a934cc7470b40a98b33
Merge: 22e6bfc 0600357
Author: Sascha Steinbiss <satta at debian.org>
Date:   Thu Aug 4 10:23:44 2016 +0000

    Merge tag 'upstream/2.1.0+ds'
    
    Upstream version 2.1.0+ds

 .travis.yml                                        |   4 -
 MANIFEST.in                                        |   1 +
 README.md                                          |   4 +-
 ariba/cluster.py                                   |   4 +-
 ariba/clusters.py                                  |  37 ++-
 ariba/ext/fml-asm_ariba.cpp                        |  14 +-
 ariba/external_progs.py                            |   4 +-
 ariba/ref_genes_getter.py                          |  74 +++++-
 ariba/ref_preparer.py                              |  11 +-
 ariba/report.py                                    |  39 ++-
 ariba/report_filter.py                             |   1 +
 ariba/samtools_variants.py                         |  17 +-
 ariba/summary.py                                   |  40 ++-
 ariba/summary_cluster.py                           |  41 +++
 ariba/summary_sample.py                            |  10 +-
 ariba/tasks/summary.py                             |   1 +
 ariba/tests/assembly_test.py                       |   6 +-
 ariba/tests/cluster_test.py                        | 189 ++++++++++++-
 ariba/tests/clusters_test.py                       |  27 ++
 .../reads_1.fq                                     | 296 +++++++++++++++++++++
 .../reads_2.fq                                     | 296 +++++++++++++++++++++
 .../references.fa                                  |   3 +
 .../reads_1.fq                                     | 296 +++++++++++++++++++++
 .../reads_2.fq                                     | 296 +++++++++++++++++++++
 .../references.fa                                  |   3 +
 .../reads_1.fq                                     | 296 +++++++++++++++++++++
 .../reads_2.fq                                     | 296 +++++++++++++++++++++
 .../references.fa                                  |   3 +
 .../reads_1.fq                                     | 296 +++++++++++++++++++++
 .../reads_2.fq                                     | 296 +++++++++++++++++++++
 .../references.fa                                  |   3 +
 .../reads_1.fq                                     | 296 +++++++++++++++++++++
 .../reads_2.fq                                     | 296 +++++++++++++++++++++
 .../references.fa                                  |   3 +
 .../reads_1.fq                                     | 296 +++++++++++++++++++++
 .../reads_2.fq                                     | 296 +++++++++++++++++++++
 .../references.fa                                  |   3 +
 ...ok_samtools_snp_known_position_pres_abs_gene.fa |   3 +
 ...s_snp_known_position_pres_abs_gene.metadata.tsv |   1 +
 ...p_known_position_pres_abs_gene.ref_for_reads.fa |  14 +
 ...mtools_snp_known_position_pres_abs_noncoding.fa |   3 +
 ..._known_position_pres_abs_noncoding.metadata.tsv |   1 +
 ...p_known_position_var_only_gene_does_have_var.fa |   3 +
 ...sition_var_only_gene_does_have_var.metadata.tsv |   1 +
 ...own_position_var_only_gene_does_not_have_var.fa |   3 +
 ...on_var_only_gene_does_not_have_var.metadata.tsv |   1 +
 ...wn_position_var_only_noncoding_does_have_var.fa |   3 +
 ...n_var_only_noncoding_does_have_var.metadata.tsv |   1 +
 ...osition_var_only_noncoding_does_not_have_var.fa |   3 +
 ...r_only_noncoding_does_not_have_var.metadata.tsv |   1 +
 ..._test_full_run_ok_samtools_snp_pres_abs_gene.fa |   3 +
 ..._run_ok_samtools_snp_pres_abs_gene.metadata.tsv |   1 +
 ..._ok_samtools_snp_pres_abs_gene.ref_for_reads.fa |  14 +
 .../reads_1.fq                                     | 296 +++++++++++++++++++++
 .../reads_2.fq                                     | 296 +++++++++++++++++++++
 .../references.fa                                  |   3 +
 ..._full_run_ok_samtools_snp_pres_abs_noncoding.fa |   3 +
 ...ok_samtools_snp_pres_abs_noncoding.metadata.tsv |   1 +
 .../reads_1.fq                                     | 296 +++++++++++++++++++++
 .../reads_2.fq                                     | 296 +++++++++++++++++++++
 .../references.fa                                  |   3 +
 ..._test_full_run_ok_samtools_snp_var_only_gene.fa |   3 +
 ..._run_ok_samtools_snp_var_only_gene.metadata.tsv |   1 +
 .../reads_1.fq                                     | 296 +++++++++++++++++++++
 .../reads_2.fq                                     | 296 +++++++++++++++++++++
 .../references.fa                                  |   3 +
 ..._full_run_ok_samtools_snp_var_only_noncoding.fa |   3 +
 ...ok_samtools_snp_var_only_noncoding.metadata.tsv |   1 +
 .../reads_1.fq                                     | 296 +++++++++++++++++++++
 .../reads_2.fq                                     | 296 +++++++++++++++++++++
 .../references.fa                                  |   3 +
 ...t_write_catted_assemblies_fasta.expected.out.fa |   6 +
 ...est_make_vcf_and_read_depths_files.expected.vcf |  29 +-
 ...mple_test_column_names_tuples_and_het_snps.tsv} |   2 +-
 .../data/summary_test_gather_output_rows.in.2.tsv  |   2 +-
 ...n.2.tsv => summary_test_get_all_het_snps.1.tsv} |   6 +-
 ...n.2.tsv => summary_test_get_all_het_snps.2.tsv} |   2 +-
 ariba/tests/ref_preparer_test.py                   |  19 +-
 ariba/tests/report_filter_test.py                  |  16 +-
 ariba/tests/samtools_variants_test.py              |   3 +-
 ariba/tests/summary_cluster_test.py                |  44 +++
 ariba/tests/summary_sample_test.py                 |  19 +-
 ariba/tests/summary_test.py                        |  19 ++
 scripts/ariba                                      |   5 +-
 setup.py                                           |   2 +-
 85 files changed, 6609 insertions(+), 107 deletions(-)

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