[med-svn] [ariba] branch master updated (cfed35a -> 452fbf3)
Sascha Steinbiss
satta at debian.org
Thu Aug 4 13:42:40 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch master
in repository ariba.
from cfed35a complete d/changelog
new 22e6bfc use zip from GitHub
new 0600357 Imported Upstream version 2.1.0+ds
new 8e6ac7f Merge tag 'upstream/2.1.0+ds'
new ec000b5 drop patches addressed upstream in 2.1.0
new be048e3 simplify manpage building
new 452fbf3 use more explicit version requirements
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:
.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 ++
debian/ariba.1.adoc | 46 +++-
debian/changelog | 7 +-
debian/control | 6 +-
debian/patches/series | 2 -
debian/rules | 2 +-
debian/watch | 2 +-
scripts/ariba | 5 +-
setup.py | 2 +-
91 files changed, 6605 insertions(+), 144 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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