[med-svn] [ariba] branch upstream updated (7e09fda -> 0600357)
Sascha Steinbiss
satta at debian.org
Thu Aug 4 13:42:41 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch upstream
in repository ariba.
from 7e09fda Imported Upstream version 2.0.0+ds
new 0600357 Imported Upstream version 2.1.0+ds
The 1 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:
.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 | 2 +-
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 2 +-
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 2 +-
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 2 +-
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 2 +-
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 2 +-
...k_samtools_snp_known_position_pres_abs_gene.fa} | 2 +-
...s_snp_known_position_pres_abs_gene.metadata.tsv | 1 +
...p_known_position_pres_abs_gene.ref_for_reads.fa | 14 +
...tools_snp_known_position_pres_abs_noncoding.fa} | 2 +-
..._known_position_pres_abs_noncoding.metadata.tsv | 1 +
..._known_position_var_only_gene_does_have_var.fa} | 2 +-
...sition_var_only_gene_does_have_var.metadata.tsv | 1 +
...wn_position_var_only_gene_does_not_have_var.fa} | 2 +-
...on_var_only_gene_does_not_have_var.metadata.tsv | 1 +
...n_position_var_only_noncoding_does_have_var.fa} | 2 +-
...n_var_only_noncoding_does_have_var.metadata.tsv | 1 +
...sition_var_only_noncoding_does_not_have_var.fa} | 2 +-
...r_only_noncoding_does_not_have_var.metadata.tsv | 1 +
...test_full_run_ok_samtools_snp_pres_abs_gene.fa} | 2 +-
..._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 | 2 +-
...full_run_ok_samtools_snp_pres_abs_noncoding.fa} | 2 +-
...ok_samtools_snp_pres_abs_noncoding.metadata.tsv | 1 +
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 2 +-
...test_full_run_ok_samtools_snp_var_only_gene.fa} | 2 +-
..._run_ok_samtools_snp_var_only_gene.metadata.tsv | 1 +
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 2 +-
...full_run_ok_samtools_snp_var_only_noncoding.fa} | 2 +-
...ok_samtools_snp_var_only_noncoding.metadata.tsv | 1 +
.../reads_1.fq | 296 +++++++++++++++++++++
.../reads_2.fq | 296 +++++++++++++++++++++
.../references.fa | 2 +-
..._write_catted_assemblies_fasta.expected.out.fa} | 0
...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.1.tsv => summary_test_get_all_het_snps.1.tsv} | 0
...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, 6561 insertions(+), 123 deletions(-)
create mode 100644 MANIFEST.in
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene/reads_2.fq
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch => cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_gene}/references.fa (90%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding/reads_2.fq
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch => cluster_test_full_run_ok_samtools_known_position_snp_pres_abs_noncoding}/references.fa (91%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var/reads_2.fq
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch => cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_have_var}/references.fa (90%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var/reads_2.fq
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch => cluster_test_full_run_ok_samtools_known_position_snp_var_only_gene_does_not_have_var}/references.fa (90%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var/reads_2.fq
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch => cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_have_var}/references.fa (91%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var/reads_2.fq
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch => cluster_test_full_run_ok_samtools_known_position_snp_var_only_noncoding_does_not_have_var}/references.fa (91%)
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch.fa => cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.fa} (90%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.metadata.tsv
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_gene.ref_for_reads.fa
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch.fa => cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.fa} (91%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_pres_abs_noncoding.metadata.tsv
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch.fa => cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.fa} (90%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_have_var.metadata.tsv
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch.fa => cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.fa} (90%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_gene_does_not_have_var.metadata.tsv
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch.fa => cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.fa} (91%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_have_var.metadata.tsv
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch.fa => cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.fa} (91%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_known_position_var_only_noncoding_does_not_have_var.metadata.tsv
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch.fa => cluster_test_full_run_ok_samtools_snp_pres_abs_gene.fa} (90%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.metadata.tsv
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene.ref_for_reads.fa
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_gene/reads_2.fq
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch => cluster_test_full_run_ok_samtools_snp_pres_abs_gene}/references.fa (90%)
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch.fa => cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.fa} (91%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding.metadata.tsv
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding/reads_2.fq
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch => cluster_test_full_run_ok_samtools_snp_pres_abs_noncoding}/references.fa (91%)
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch.fa => cluster_test_full_run_ok_samtools_snp_var_only_gene.fa} (90%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene.metadata.tsv
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_gene/reads_2.fq
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch => cluster_test_full_run_ok_samtools_snp_var_only_gene}/references.fa (90%)
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch.fa => cluster_test_full_run_ok_samtools_snp_var_only_noncoding.fa} (91%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding.metadata.tsv
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_ok_samtools_snp_var_only_noncoding/reads_2.fq
copy ariba/tests/data/{cluster_test_full_run_ok_gene_start_mismatch => cluster_test_full_run_ok_samtools_snp_var_only_noncoding}/references.fa (91%)
copy ariba/tests/data/{clusters_test_write_catted_assembled_genes_fasta.expected.out.fa => clusters_test_write_catted_assemblies_fasta.expected.out.fa} (100%)
rename ariba/tests/data/{summary_sample_test_column_names_tuples.tsv => summary_sample_test_column_names_tuples_and_het_snps.tsv} (90%)
copy ariba/tests/data/{summary_test_gather_output_rows.in.1.tsv => summary_test_get_all_het_snps.1.tsv} (100%)
copy ariba/tests/data/{summary_test_gather_output_rows.in.2.tsv => summary_test_get_all_het_snps.2.tsv} (84%)
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