[med-svn] [ariba] branch master updated (439724e -> f85b24c)

[Sascha Steinbiss]

This is an automated email from the git hooks/post-receive script.

satta pushed a change to branch master
in repository ariba.

      from  439724e   Debian version bump
       new  d73cf5b   Imported Upstream version 2.2.5+ds
       new  5d619c8   Merge tag 'upstream/2.2.5+ds'
       new  65b36b5   remove deps on samtools and bcftools
       new  e161880   refresh patches
       new  3d7371c   Debian version bump
       new  f85b24c   fix Debian version

The 6 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                                          |   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 +
 debian/changelog                                   |    7 +
 debian/control                                     |    4 -
 debian/patches/rename-cdhit.patch                  |    4 +-
 .../use_debian_packaged_libs_for_extension.patch   |    2 +-
 install_dependencies.sh                            |   25 -
 scripts/ariba                                      |    1 -
 setup.py                                           |   10 +-
 43 files changed, 11996 insertions(+), 469 deletions(-)
 delete mode 100644 ariba/best_seq_chooser.py
 create mode 100644 ariba/ext/vcfcall_ariba.cpp
 delete mode 100644 ariba/tests/best_seq_chooser_test.py
 create mode 100644 ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov
 delete mode 100644 ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz.tbi
 create mode 100644 ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa
 create mode 100644 ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq
 create mode 100644 ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq
 create mode 100644 ariba/tests/data/summary_test_whole_run.in.1.tsv
 create mode 100644 ariba/tests/data/summary_test_whole_run.in.2.tsv
 create mode 100644 ariba/tests/data/summary_test_whole_run.out.csv

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