[med-svn] [ariba] branch upstream updated (d73cf5b -> 4c36268)
Sascha Steinbiss
satta at debian.org
Wed Oct 12 16:10:36 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 d73cf5b Imported Upstream version 2.2.5+ds
new 4c36268 New upstream version 2.3.0+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
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Summary of changes:
Dockerfile | 19 +
README.md | 38 +-
ariba/assembly.py | 18 +-
ariba/cluster.py | 24 +-
ariba/clusters.py | 15 +-
ariba/ext/minimap_ariba.cpp | 51 +-
ariba/external_progs.py | 6 +-
ariba/mash.py | 15 +-
ariba/ref_genes_getter.py | 43 +-
ariba/ref_preparer.py | 13 +-
ariba/reference_data.py | 18 +-
ariba/report.py | 188 ++++---
ariba/samtools_variants.py | 5 +-
ariba/summary.py | 20 +-
ariba/summary_cluster.py | 101 ++--
ariba/summary_cluster_variant.py | 67 ++-
ariba/tasks/getref.py | 3 +-
ariba/tasks/prepareref.py | 1 +
ariba/tasks/run.py | 4 +
ariba/test_run_data/metadata.tsv | 1 +
ariba/test_run_data/reads_1.fq | 4 +
ariba/test_run_data/reads_2.fq | 4 +
.../test_run_data/ref_fasta_to_make_reads_from.fa | 5 +
ariba/test_run_data/ref_seqs.fa | 5 +
ariba/tests/assembly_test.py | 14 +-
ariba/tests/cluster_test.py | 133 +++--
ariba/tests/clusters_test.py | 11 +
.../data/cluster_test_full_run_delete_codon.fa | 3 +
....tsv => cluster_test_full_run_delete_codon.tsv} | 0
.../for_reads.fa | 20 +
.../cluster_test_full_run_delete_codon/reads_1.fq | 588 ++++++++++++++++++++
.../cluster_test_full_run_delete_codon/reads_2.fq | 588 ++++++++++++++++++++
.../references.fa | 3 +
.../data/cluster_test_full_run_insert_codon.fa | 3 +
....tsv => cluster_test_full_run_insert_codon.tsv} | 0
.../for_reads.fa | 20 +
.../cluster_test_full_run_insert_codon/reads_1.fq | 592 +++++++++++++++++++++
.../cluster_test_full_run_insert_codon/reads_2.fq | 592 +++++++++++++++++++++
.../references.fa | 3 +
...e.fa => cluster_test_full_run_multiple_vars.fa} | 0
...tsv => cluster_test_full_run_multiple_vars.tsv} | 1 +
.../for_reads.fa | 20 +
.../cluster_test_full_run_multiple_vars/reads_1.fq | 584 ++++++++++++++++++++
.../cluster_test_full_run_multiple_vars/reads_2.fq | 584 ++++++++++++++++++++
.../references.fa | 0
.../data/cluster_test_full_run_ok_non_coding.fa | 2 +-
...cluster_test_full_run_ref_not_in_cluster.in.fa} | 0
...luster_test_full_run_ref_not_in_cluster.in.tsv} | 0
...uster_test_full_run_ref_not_in_cluster.mash.fa} | 5 +-
...er_test_full_run_ref_not_in_cluster.mash.fa.msh | Bin 0 -> 2760 bytes
.../reads_1.fq | 0
.../reads_2.fq | 0
.../references.fa | 0
...sters_minimap_reads_to_all_refs.out.clstr_count | 4 +-
.../clusters_minimap_reads_to_all_refs.out.hist | 37 +-
ariba/tests/data/clusters_test_dummy_db.fa.msh | Bin 0 -> 504 bytes
ariba/tests/data/clusters_test_write_report.tsv | 2 +-
ariba/tests/data/reference_data_init_ok.rename.tsv | 2 +
.../tests/data/reference_data_load_rename_file.tsv | 2 +
ariba/tests/data/report_filter_test_init_bad.tsv | 8 +-
ariba/tests/data/report_filter_test_init_good.tsv | 10 +-
.../data/report_filter_test_load_report_bad.tsv | 8 +-
.../data/report_filter_test_load_report_good.tsv | 10 +-
.../tests/data/report_filter_test_run.expected.tsv | 12 +-
ariba/tests/data/report_filter_test_run.in.tsv | 18 +-
.../tests/data/report_filter_test_write_report.tsv | 8 +-
.../summary_gather_unfiltered_output_data.in.1.tsv | 12 +-
.../summary_gather_unfiltered_output_data.in.2.tsv | 12 +-
...ample_test_column_names_tuples_and_het_snps.tsv | 16 +-
.../summary_sample_test_column_summary_data.tsv | 16 +-
.../data/summary_sample_test_load_file.in.tsv | 14 +-
.../summary_sample_test_non_synon_variants.tsv | 12 +-
.../tests/data/summary_sample_test_var_groups.tsv | 14 +-
.../tests/data/summary_test_load_input_files.1.tsv | 6 +-
.../tests/data/summary_test_load_input_files.2.tsv | 10 +-
ariba/tests/data/summary_test_whole_run.in.1.tsv | 34 +-
ariba/tests/data/summary_test_whole_run.in.2.tsv | 15 +-
ariba/tests/data/summary_test_whole_run.out.csv | 6 +-
ariba/tests/data/summary_to_matrix.1.tsv | 10 +-
ariba/tests/data/summary_to_matrix.2.tsv | 12 +-
ariba/tests/read_filter_test.py | 8 +-
ariba/tests/ref_preparer_test.py | 1 +
ariba/tests/reference_data_test.py | 17 +
ariba/tests/report_filter_test.py | 58 +-
ariba/tests/samtools_variants_test.py | 22 +-
ariba/tests/summary_cluster_test.py | 248 +++++----
ariba/tests/summary_cluster_variant_test.py | 73 ++-
ariba/tests/summary_test.py | 56 +-
scripts/ariba | 61 ++-
setup.py | 2 +-
90 files changed, 4671 insertions(+), 619 deletions(-)
create mode 100644 Dockerfile
create mode 100644 ariba/tests/data/cluster_test_full_run_delete_codon.fa
copy ariba/tests/data/{cluster_test_full_run_partial_asmbly.tsv => cluster_test_full_run_delete_codon.tsv} (100%)
create mode 100644 ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa
create mode 100644 ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_delete_codon/references.fa
create mode 100644 ariba/tests/data/cluster_test_full_run_insert_codon.fa
copy ariba/tests/data/{cluster_test_full_run_partial_asmbly.tsv => cluster_test_full_run_insert_codon.tsv} (100%)
create mode 100644 ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa
create mode 100644 ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_insert_codon/references.fa
copy ariba/tests/data/{cluster_test_full_run_ok_presence_absence.fa => cluster_test_full_run_multiple_vars.fa} (100%)
copy ariba/tests/data/{cluster_test_full_run_partial_asmbly.tsv => cluster_test_full_run_multiple_vars.tsv} (50%)
create mode 100644 ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa
create mode 100644 ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq
create mode 100644 ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq
copy ariba/tests/data/{cluster_test_full_run_ok_presence_absence => cluster_test_full_run_multiple_vars}/references.fa (100%)
copy ariba/tests/data/{cluster_test_full_run_ok_non_coding/references.fa => cluster_test_full_run_ref_not_in_cluster.in.fa} (100%)
copy ariba/tests/data/{cluster_test_full_run_ok_non_coding.metadata.tsv => cluster_test_full_run_ref_not_in_cluster.in.tsv} (100%)
copy ariba/tests/data/{cluster_test_full_run_ok_non_coding/references.fa => cluster_test_full_run_ref_not_in_cluster.mash.fa} (65%)
create mode 100644 ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.mash.fa.msh
copy ariba/tests/data/{cluster_test_full_run_ok_non_coding => cluster_test_full_run_ref_not_in_cluster}/reads_1.fq (100%)
copy ariba/tests/data/{cluster_test_full_run_ok_non_coding => cluster_test_full_run_ref_not_in_cluster}/reads_2.fq (100%)
copy ariba/tests/data/{cluster_test_full_run_ok_non_coding => cluster_test_full_run_ref_not_in_cluster}/references.fa (100%)
create mode 100644 ariba/tests/data/clusters_test_dummy_db.fa.msh
create mode 100644 ariba/tests/data/reference_data_init_ok.rename.tsv
create mode 100644 ariba/tests/data/reference_data_load_rename_file.tsv
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