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satta pushed a change to branch master
in repository ariba.
from f85b24c fix Debian version
new 4c36268 New upstream version 2.3.0+ds
new efc4d60 Merge tag 'upstream/2.3.0+ds'
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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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