[med-svn] [ariba] 03/05: Merge tag 'upstream/1.0.0'
Sascha Steinbiss
sascha at steinbiss.name
Fri May 27 14:13:04 UTC 2016
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sascha-guest pushed a commit to branch master
in repository ariba.
commit 37d3682a1b52aa01a339c97e76298a7296ce8809
Merge: 68e7acf 194d86c
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Fri May 27 11:01:29 2016 +0000
Merge tag 'upstream/1.0.0'
Upstream version 1.0.0
.travis.yml | 23 +
README.md | 67 +-
ariba/__init__.py | 28 +-
ariba/aln_to_metadata.py | 269 ++++
ariba/assembly.py | 377 ++++++
ariba/assembly_compare.py | 371 ++++++
ariba/assembly_variants.py | 323 +++++
ariba/best_seq_chooser.py | 98 ++
ariba/card_record.py | 111 ++
ariba/cdhit.py | 199 +--
ariba/cluster.py | 1319 +++++---------------
ariba/clusters.py | 674 ++++++----
ariba/common.py | 31 +-
ariba/external_progs.py | 224 ++--
ariba/faidx.py | 5 +-
ariba/flag.py | 9 +-
ariba/mapping.py | 196 +--
ariba/read_store.py | 60 +
ariba/ref_genes_getter.py | 267 ++++
ariba/ref_preparer.py | 189 +++
ariba/refcheck.py | 90 --
ariba/reference_data.py | 510 ++++++++
ariba/report.py | 268 ++++
ariba/report_filter.py | 216 ++++
ariba/samtools_variants.py | 194 +++
ariba/sequence_metadata.py | 48 +
ariba/sequence_variant.py | 70 ++
ariba/summary.py | 480 ++++---
ariba/summary_cluster.py | 258 ++++
ariba/summary_sample.py | 61 +
ariba/tasks/aln2meta.py | 28 +
ariba/tasks/getref.py | 19 +
ariba/tasks/prepareref.py | 59 +
ariba/tasks/refcheck.py | 31 -
ariba/tasks/reportfilter.py | 35 +
ariba/tasks/run.py | 90 +-
ariba/tasks/summary.py | 108 +-
ariba/tasks/test.py | 94 ++
ariba/tasks/version.py | 6 +-
ariba/test_run_data/metadata.tsv | 14 +
ariba/test_run_data/non_coding.fa | 10 +
ariba/test_run_data/presence_absence.fa | 5 +
ariba/test_run_data/reads_1.fq | 908 ++++++++++++++
ariba/test_run_data/reads_2.fq | 908 ++++++++++++++
.../test_run_data/ref_fasta_to_make_reads_from.fa | 36 +
ariba/test_run_data/variants_only.fa | 6 +
ariba/tests/aln_to_metadata_test.py | 411 ++++++
ariba/tests/assembly_compare_test.py | 381 ++++++
ariba/tests/assembly_test.py | 135 ++
ariba/tests/assembly_variants_test.py | 385 ++++++
ariba/tests/best_seq_chooser_test.py | 69 +
ariba/tests/card_record_test.py | 205 +++
ariba/tests/cdhit_test.py | 130 +-
ariba/tests/cluster_test.py | 967 +++-----------
ariba/tests/clusters_test.py | 199 ++-
ariba/tests/common_test.py | 22 +
.../tests/data/aln_to_metadata_load_aln_file.in.fa | 4 +
.../data/aln_to_metadata_load_vars_file_bad.1.tsv | 2 +
.../data/aln_to_metadata_load_vars_file_bad.2.tsv | 2 +
.../data/aln_to_metadata_load_vars_file_good.tsv | 3 +
.../data/aln_to_metadata_make_cluster_file.out | 1 +
ariba/tests/data/aln_to_metadata_run_coding.in.fa | 10 +
ariba/tests/data/aln_to_metadata_run_coding.in.tsv | 2 +
.../data/aln_to_metadata_run_coding.out.cluster | 1 +
ariba/tests/data/aln_to_metadata_run_coding.out.fa | 10 +
.../tests/data/aln_to_metadata_run_coding.out.tsv | 7 +
.../tests/data/aln_to_metadata_run_noncoding.in.fa | 10 +
.../data/aln_to_metadata_run_noncoding.in.tsv | 2 +
.../data/aln_to_metadata_run_noncoding.out.cluster | 1 +
.../data/aln_to_metadata_run_noncoding.out.fa | 10 +
.../data/aln_to_metadata_run_noncoding.out.tsv | 7 +
...ssembly_compare_parse_nucmer_coords_file.coords | 7 +
... assembly_test_assemble_with_spades_reads_1.fq} | 0
... assembly_test_assemble_with_spades_reads_2.fq} | 0
...a => assembly_test_assemble_with_spades_ref.fa} | 0
.../assembly_test_check_spades_log_file.log.bad | 5 +
.../assembly_test_check_spades_log_file.log.good | 5 +
... => assembly_test_fix_contig_orientation.in.fa} | 7 +
...=> assembly_test_fix_contig_orientation.out.fa} | 7 +
...=> assembly_test_fix_contig_orientation.ref.fa} | 0
...st_gapfill_with_gapfiller.scaffolds_no_gaps.fa} | 0
..._gapfill_with_gapfiller.scaffolds_with_gaps.fa} | 0
...ssembly_test_gapfill_with_gapfiller_reads_1.fq} | 0
...ssembly_test_gapfill_with_gapfiller_reads_2.fq} | 0
.../assembly_test_has_gaps_to_fill.has_gaps.fa | 2 +
.../data/assembly_test_has_gaps_to_fill.no_gaps.fa | 4 +
...> assembly_test_parse_assembly_bam.assembly.fa} | 0
...am.bam => assembly_test_parse_assembly_bam.bam} | Bin
....in.fa => assembly_test_rename_scaffolds.in.fa} | 0
.../data/assembly_test_rename_scaffolds.out.fa | 6 +
... assembly_test_scaffold_with_sspace_contigs.fa} | 0
... assembly_test_scaffold_with_sspace_reads_1.fq} | 0
... assembly_test_scaffold_with_sspace_reads_2.fq} | 0
... => assembly_test_set_assembly_kmer_reads_1.fq} | 0
... => assembly_test_set_assembly_kmer_reads_2.fq} | 0
...ly_variants_test_get_mummer_variants.none.snps} | 0
...bly_variants_test_get_mummer_variants.snp.snps} | 0
..._one_variant_for_one_contig_coding_metadata.tsv | 11 +
...riant_for_one_contig_coding_presence_absence.fa | 2 +
..._variant_for_one_contig_non_coding.metadata.tsv | 11 +
...sembly_variants_test_get_variants_non_coding.fa | 2 +
..._variants_test_get_variants_presence_absence.fa | 2 +
...ariants_test_get_variants_presence_absence.snps | 3 +
...bly_variants_test_get_variants_variants_only.fa | 2 +
...y_variants_test_get_variants_variants_only.snps | 3 +
...s_1.fq => best_seq_chooser_best_seq_reads_1.fq} | 0
...s_2.fq => best_seq_chooser_best_seq_reads_2.fq} | 0
.../genes.fa => best_seq_chooser_best_seq_ref.fa} | 0
.../data/best_seq_chooser_best_seq_ref.fa.fai | 3 +
...ser_get_best_seq_by_alignment_score_reads_1.fq} | 0
...ser_get_best_seq_by_alignment_score_reads_2.fq} | 0
...chooser_get_best_seq_by_alignment_score_ref.fa} | 0
...oser_get_best_seq_by_alignment_score_ref.fa.fai | 3 +
...t_seq_chooser_total_alignment_score_reads_1.fq} | 0
...t_seq_chooser_total_alignment_score_reads_2.fq} | 0
..._seq_chooser_total_alignment_score_ref_seqs.fa} | 0
...q_chooser_total_alignment_score_ref_seqs.fa.fai | 3 +
ariba/tests/data/cdhit_test_enumerate_fasta.in.fa | 6 -
ariba/tests/data/cdhit_test_enumerate_fasta.out.fa | 6 -
ariba/tests/data/cdhit_test_fake_run.out.fa | 8 +-
.../data/cdhit_test_load_user_clusters_file.bad1 | 1 +
.../data/cdhit_test_load_user_clusters_file.bad2 | 2 +
.../data/cdhit_test_load_user_clusters_file.bad3 | 2 +
.../data/cdhit_test_load_user_clusters_file.good | 3 +
.../data/cdhit_test_parse_cluster_info_file.in.fa | 40 -
...dhit_test_parse_cluster_info_file.in.renamed.fa | 40 -
.../data/cdhit_test_parse_cluster_info_file.infile | 6 +
.../data/cdhit_test_parse_cluster_info_file.out.fa | 20 -
...t_test_parse_cluster_info_file.out.fa.bak.clstr | 4 -
.../data/cdhit_test_rename_clusters.expected.fa | 6 +
ariba/tests/data/cdhit_test_rename_clusters.in.fa | 6 +
ariba/tests/data/cdhit_test_rename_fasta.in.fa | 6 -
ariba/tests/data/cdhit_test_run.out.fa | 4 +-
...hit_test_run_get_clusters_from_dict.in.clusters | 2 +
...=> cdhit_test_run_get_clusters_from_dict.in.fa} | 6 +-
.../cdhit_test_run_get_clusters_from_dict.out.fa | 4 +
.../cluster_test_assemble_with_spades/genes.fa | 2 -
.../data/cluster_test_choose_best_gene.gene.fa | 6 -
ariba/tests/data/cluster_test_count_reads_1.fq | 8 +
ariba/tests/data/cluster_test_count_reads_2.fq | 8 +
.../cluster_test_fix_contig_orientation/genes.fa | 10 -
...luster_test_full_run_assembly_fail.noncoding.fa | 8 +
.../cluster_test_full_run_assembly_fail/reads_1.fq | 8 +
.../cluster_test_full_run_assembly_fail/reads_2.fq | 8 +
.../references.fa | 8 +
...st_full_run_choose_ref_fail.presence_absence.fa | 2 +
.../reads_1.fq | 4 +
.../reads_2.fq | 4 +
.../references.fa | 4 +
.../data/cluster_test_full_run_ok_non_coding.fa | 6 +
...luster_test_full_run_ok_non_coding.metadata.tsv | 5 +
.../cluster_test_full_run_ok_non_coding/reads_1.fq | 144 +++
.../cluster_test_full_run_ok_non_coding/reads_2.fq | 144 +++
.../references.fa | 6 +
.../cluster_test_full_run_ok_presence_absence.fa | 5 +
..._test_full_run_ok_presence_absence.metadata.tsv | 4 +
.../reads_1.fq | 128 ++
.../reads_2.fq | 128 ++
.../references.fa | 5 +
.../data/cluster_test_full_run_ok_variants_only.fa | 5 +
...nts_only.not_present.always_report.metadata.tsv | 2 +
...l_run_ok_variants_only.not_present.metadata.tsv | 2 +
..._full_run_ok_variants_only.present.metadata.tsv | 3 +
.../reads_1.fq | 132 ++
.../reads_2.fq | 132 ++
.../references.fa | 5 +
.../cluster_test_gapfill_with_gapfiller.gene.fa | 2 -
.../cluster_test_gapfill_with_gapfiller/genes.fa | 2 -
ariba/tests/data/cluster_test_generic/genes.fa | 2 -
ariba/tests/data/cluster_test_generic/reads_1.fq | 4 -
ariba/tests/data/cluster_test_generic/reads_2.fq | 4 -
.../data/cluster_test_get_read_counts/genes.fa | 2 -
.../data/cluster_test_get_read_counts/reads_1.fq | 4 -
.../data/cluster_test_get_read_counts/reads_2.fq | 4 -
.../cluster_test_get_read_counts_fail/genes.fa | 2 -
.../cluster_test_get_read_counts_fail/reads_1.fq | 8 -
.../cluster_test_get_read_counts_fail/reads_2.fq | 4 -
.../reads_1.fq | 0
.../reads_2.fq | 0
ariba/tests/data/cluster_test_init_refdata.fa | 2 +
.../cluster_test_load_final_contigs.contigs.fa | 6 -
.../data/cluster_test_load_final_contigs/genes.fa | 2 -
.../cluster_test_load_final_contigs/reads_1.fq | 4 -
.../cluster_test_load_final_contigs/reads_2.fq | 4 -
.../cluster_test_make_reads_for_assembly.in1.fq | 40 +
.../cluster_test_make_reads_for_assembly.in2.fq | 40 +
.../cluster_test_make_reads_for_assembly.out1.fq | 28 +
.../cluster_test_make_reads_for_assembly.out2.fq | 28 +
.../cluster_test_make_report_lines.read_depths.gz | Bin 78 -> 0 bytes
...uster_test_make_report_lines.read_depths.gz.tbi | Bin 91 -> 0 bytes
...its_to_assembled_gene_sequences.expected.out.fa | 7 -
...luster_test_number_of_reads_for_assembly.ref.fa | 3 +
.../data/cluster_test_parse_assembly_bam/genes.fa | 2 -
.../cluster_test_parse_assembly_bam/reads_1.fq | 4 -
.../cluster_test_parse_assembly_bam/reads_2.fq | 4 -
...uster_test_parse_assembly_vs_gene_coords.coords | 7 -
.../genes.fa | 2 -
.../reads_1.fq | 4 -
.../reads_2.fq | 4 -
.../data/cluster_test_rename_scaffolds.out.fa | 6 -
.../data/cluster_test_rename_scaffolds/genes.fa | 2 -
.../data/cluster_test_rename_scaffolds/reads_1.fq | 4 -
.../data/cluster_test_rename_scaffolds/reads_2.fq | 4 -
.../data/cluster_test_scaffold_with_sspace.gene.fa | 2 -
.../cluster_test_scaffold_with_sspace/genes.fa | 2 -
.../data/cluster_test_set_assembly_kmer/genes.fa | 2 -
.../data/cluster_test_set_assembly_kmer/reads_1.fq | 12 -
.../data/cluster_test_set_assembly_kmer/reads_2.fq | 12 -
...usters_test_bam_to_clusters.out.ref2.reads_1.fq | 4 -
...usters_test_bam_to_clusters.out.ref2.reads_2.fq | 4 -
.../clusters_test_bam_to_clusters_reads.db.fa.fai | 3 +
...usters_test_bam_to_clusters_reads.read_store.gz | Bin 0 -> 213 bytes
...ers_test_bam_to_clusters_reads_no_reads_map.bam | Bin 0 -> 364 bytes
...s_test_bam_to_clusters_reads_no_reads_map_1.fq} | 4 +-
...s_test_bam_to_clusters_reads_no_reads_map_2.fq} | 4 +-
ariba/tests/data/clusters_test_dummy_db.fa | 2 +
ariba/tests/data/clusters_test_load_data_info_file | 5 +
.../cdhit.clusters.pickle | Bin 0 -> 34 bytes
.../info.txt | 5 +
.../refcheck.01.check_variants.non_coding.fa | 2 +
.../refcheck.01.check_variants.presence_absence.fa | 2 +
.../refcheck.01.check_variants.tsv | 2 +
.../refcheck.01.check_variants.variants_only.fa | 2 +
...te_catted_assembled_genes_fasta.expected.out.fa | 10 +-
..._write_catted_assembled_genes_fasta.in.gene1.fa | 4 -
..._write_catted_assembled_genes_fasta.in.gene2.fa | 2 -
...atted_genes_matching_refs_fasta.expected.out.fa | 4 +
ariba/tests/data/clusters_test_write_report.tsv | 6 +-
...ing_test_bowtie2_remove_both_unmapped_reads.bam | Bin 0 -> 422 bytes
...ng_test_bowtie2_remove_both_unmapped_reads_1.fq | 16 +
...ng_test_bowtie2_remove_both_unmapped_reads_2.fq | 16 +
...ert.bam => mapping_test_sam_pair_to_insert.bam} | Bin
..._to_fastq.bam => mapping_test_sam_to_fastq.bam} | Bin
ariba/tests/data/mapping_test_smalt_reads_1.fq | 28 -
ariba/tests/data/mapping_test_smalt_reads_2.fq | 28 -
ariba/tests/data/mapping_test_smalt_ref.fa | 5 -
ariba/tests/data/mapping_test_smalt_ref.fa.fai | 1 -
ariba/tests/data/mapping_test_smalt_sorted.bam | Bin 648 -> 0 bytes
ariba/tests/data/mapping_test_smalt_unsorted.bam | Bin 656 -> 0 bytes
ariba/tests/data/read_store_test_clean.in | 10 +
.../read_store_test_compress_and_index_file.in | 10 +
ariba/tests/data/read_store_test_get_reads.in | 10 +
.../data/read_store_test_get_reads.reads_1.fq | 12 +
.../data/read_store_test_get_reads.reads_2.fq | 12 +
ariba/tests/data/read_store_test_sort_file.in | 10 +
ariba/tests/data/read_store_test_sort_file.out | 10 +
.../data/ref_preparer_test_write_info_file.out | 5 +
...ence_data_filter_bad_data_metadata.expected.tsv | 9 +
.../reference_data_filter_bad_data_metadata.in.tsv | 20 +
...nce_data_filter_bad_data_non_coding.expected.fa | 2 +
...reference_data_filter_bad_data_non_coding.in.fa | 2 +
...ta_filter_bad_data_presence_absence.expected.fa | 6 +
...nce_data_filter_bad_data_presence_absence.in.fa | 6 +
..._data_filter_bad_data_variants_only.expected.fa | 2 +
...erence_data_filter_bad_data_variants_only.in.fa | 6 +
ariba/tests/data/reference_data_get_filename | 1 +
ariba/tests/data/reference_data_init.tsv | 4 +
.../reads_1.fq => reference_data_init_empty.fa} | 0
.../data/reference_data_init_presence_absence.fa | 4 +
.../data/reference_data_keep_seqs_from_dict.fa | 2 +
.../data/reference_data_keep_seqs_from_dict.log | 1 +
ariba/tests/data/reference_data_load_fasta_file.fa | 2 +
.../data/reference_data_load_metadata_tsv.tsv | 3 +
.../reference_data_make_catted_fasta.expected.fa | 6 +
.../reference_data_make_catted_fasta.noncoding.fa | 2 +
...ence_data_make_catted_fasta.presence_absence.fa | 2 +
...ference_data_make_catted_fasta.variants_only.fa | 2 +
.../data/reference_data_remove_bad_genes.in.fa | 10 +
.../reference_data_rename_sequences.noncoding.fa | 4 +
...rence_data_rename_sequences.presence_absence.fa | 10 +
...eference_data_rename_sequences.variants_only.fa | 8 +
.../reference_data_rename_sequences_metadata.tsv | 11 +
.../reference_data_sequence.presence_absence.fa | 2 +
...erence_data_sequence_length.presence_absence.fa | 2 +
.../data/reference_data_sequence_type.noncoding.fa | 2 +
...eference_data_sequence_type.presence_absence.fa | 2 +
.../reference_data_sequence_type.variants_only.fa | 2 +
...est_all_non_wild_type_variants.ref.noncoding.fa | 2 +
...test_all_non_wild_type_variants.ref.pres_abs.fa | 2 +
...test_all_non_wild_type_variants.ref.var_only.fa | 2 +
...erence_data_test_all_non_wild_type_variants.tsv | 12 +
...rence_data_test_cluster_with_cdhit.clusters.tsv | 3 +
..._cluster_with_cdhit.expected_representatives.fa | 10 +
...ence_data_test_cluster_with_cdhit.non_coding.fa | 5 +
...ata_test_cluster_with_cdhit.presence_absence.fa | 10 +
...st_cluster_with_cdhit_clusters_in_file.clusters | 4 +
...luster_with_cdhit_clusters_in_file.clusters.tsv | 4 +
...it_clusters_in_file.expected_representatives.fa | 16 +
...uster_with_cdhit_clusters_in_file.non_coding.fa | 10 +
...with_cdhit_clusters_in_file.presence_absence.fa | 10 +
..._test_cluster_with_cdhit_nocluster.clusters.tsv | 6 +
...ith_cdhit_nocluster.expected_representatives.fa | 20 +
...test_cluster_with_cdhit_nocluster.non_coding.fa | 10 +
...luster_with_cdhit_nocluster.presence_absence.fa | 10 +
.../data/reference_data_test_remove_bad_genes.log | 5 +
.../data/reference_data_test_rename_sequences.out | 8 +
...ata_test_write_cluster_allocation_file.expected | 4 +
...rence_data_test_write_seqs_to_fasta.expected.fa | 6 +
.../reference_data_test_write_seqs_to_fasta.in.fa | 10 +
...a => reference_data_write_dict_of_sequences.fa} | 6 +-
.../reference_data_write_metadata_tsv.expected.tsv | 2 +
.../data/reference_data_write_metadata_tsv.tsv | 2 +
...nce_data_write_metadata_tsv_presence_absence.fa | 4 +
ariba/tests/data/report_filter_test_init_bad.tsv | 4 +
ariba/tests/data/report_filter_test_init_good.tsv | 5 +
.../data/report_filter_test_load_report_bad.tsv | 4 +
.../data/report_filter_test_load_report_good.tsv | 5 +
.../tests/data/report_filter_test_run.expected.tsv | 6 +
ariba/tests/data/report_filter_test_run.in.tsv | 9 +
.../tests/data/report_filter_test_write_report.tsv | 4 +
...mtools_variants_test_get_depths_at_position.bam | Bin 0 -> 4744 bytes
...ols_variants_test_get_depths_at_position.ref.fa | 18 +
...variants_test_get_depths_at_position.ref.fa.fai | 1 +
...z => samtools_variants_test_get_read_depths.gz} | Bin
... samtools_variants_test_get_read_depths.gz.tbi} | Bin
...riants_test_get_variant_positions_from_vcf.vcf} | 0
...ools_variants_test_get_variants.read_depths.gz} | Bin
..._variants_test_get_variants.read_depths.gz.tbi} | Bin
...vcf => samtools_variants_test_get_variants.vcf} | 0
...est_make_vcf_and_read_depths_files.assembly.fa} | 0
...make_vcf_and_read_depths_files.assembly.fa.fai} | 0
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..._and_read_depths_files.expected.read_depths.gz} | Bin
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...st_make_vcf_and_read_depths_files.expected.vcf} | 0
.../samtools_variants_test_total_depth_per_contig | 7 +
... samtools_variants_test_variants_in_coords.vcf} | 0
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.../data/summary_sample_test_load_file.in.tsv | 7 +
.../summary_sample_test_non_synon_variants.tsv | 8 +
.../tests/data/summary_sample_test_var_groups.tsv | 7 +
.../data/summary_test_gather_output_rows.in.1.tsv | 7 +-
.../data/summary_test_gather_output_rows.in.2.tsv | 8 +-
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ariba/tests/data/summary_test_load_file.in.tsv | 5 -
.../tests/data/summary_test_load_input_files.1.tsv | 3 +
.../tests/data/summary_test_load_input_files.2.tsv | 5 +
.../summary_test_newick_from_dist_matrix.distances | 4 +
.../data/summary_test_newick_from_dist_matrix.tre | 1 +
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ariba/tests/data/test_common_cat_files.in.2 | 3 +
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ariba/tests/data/test_common_cat_files.out | 6 +
ariba/tests/data/vfdb_parser_test_run.in.fa | 6 +
ariba/tests/data/vfdb_parser_test_run.out.fa | 6 +
ariba/tests/data/vfdb_parser_test_run.out.tsv | 2 +
ariba/tests/external_progs_test.py | 9 +
ariba/tests/faidx_test.py | 5 +-
ariba/tests/flag_test.py | 11 +-
ariba/tests/mapping_test.py | 134 +-
ariba/tests/read_store_test.py | 80 ++
ariba/tests/ref_preparer_test.py | 121 ++
ariba/tests/refcheck_test.py | 69 -
ariba/tests/reference_data_test.py | 678 ++++++++++
ariba/tests/report_filter_test.py | 335 +++++
ariba/tests/samtools_variants_test.py | 173 +++
ariba/tests/sequence_metadata_test.py | 89 ++
ariba/tests/sequence_variant_test.py | 100 ++
ariba/tests/summary_cluster_test.py | 424 +++++++
ariba/tests/summary_sample_test.py | 104 ++
ariba/tests/summary_test.py | 503 ++++++--
ariba/tests/versions_test.py | 8 +
ariba/tests/vfdb_parser_test.py | 60 +
ariba/versions.py | 66 +
ariba/vfdb_parser.py | 46 +
install_dependencies.sh | 115 ++
scripts/ariba | 14 +-
setup.py | 11 +-
374 files changed, 14344 insertions(+), 3389 deletions(-)
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