Lista plików pakietu ariba z gałęzi sid na architekturę alpha

/usr/bin/ariba
/usr/lib/python3/dist-packages/ariba-2.14.6.egg-info/PKG-INFO
/usr/lib/python3/dist-packages/ariba-2.14.6.egg-info/dependency_links.txt
/usr/lib/python3/dist-packages/ariba-2.14.6.egg-info/requires.txt
/usr/lib/python3/dist-packages/ariba-2.14.6.egg-info/top_level.txt
/usr/lib/python3/dist-packages/ariba/__init__.py
/usr/lib/python3/dist-packages/ariba/aln_to_metadata.py
/usr/lib/python3/dist-packages/ariba/assembly.py
/usr/lib/python3/dist-packages/ariba/assembly_compare.py
/usr/lib/python3/dist-packages/ariba/assembly_variants.py
/usr/lib/python3/dist-packages/ariba/bam_parse.py
/usr/lib/python3/dist-packages/ariba/card_record.py
/usr/lib/python3/dist-packages/ariba/cdhit.py
/usr/lib/python3/dist-packages/ariba/cluster.py
/usr/lib/python3/dist-packages/ariba/clusters.py
/usr/lib/python3/dist-packages/ariba/common.py
/usr/lib/python3/dist-packages/ariba/external_progs.py
/usr/lib/python3/dist-packages/ariba/faidx.py
/usr/lib/python3/dist-packages/ariba/flag.py
/usr/lib/python3/dist-packages/ariba/histogram.py
/usr/lib/python3/dist-packages/ariba/link.py
/usr/lib/python3/dist-packages/ariba/mapping.py
/usr/lib/python3/dist-packages/ariba/megares_data_finder.py
/usr/lib/python3/dist-packages/ariba/megares_zip_parser.py
/usr/lib/python3/dist-packages/ariba/mic_plotter.py
/usr/lib/python3/dist-packages/ariba/mlst_profile.py
/usr/lib/python3/dist-packages/ariba/mlst_reporter.py
/usr/lib/python3/dist-packages/ariba/pubmlst_getter.py
/usr/lib/python3/dist-packages/ariba/pubmlst_ref_preparer.py
/usr/lib/python3/dist-packages/ariba/read_filter.py
/usr/lib/python3/dist-packages/ariba/read_store.py
/usr/lib/python3/dist-packages/ariba/ref_genes_getter.py
/usr/lib/python3/dist-packages/ariba/ref_preparer.py
/usr/lib/python3/dist-packages/ariba/ref_seq_chooser.py
/usr/lib/python3/dist-packages/ariba/refdata_query.py
/usr/lib/python3/dist-packages/ariba/reference_data.py
/usr/lib/python3/dist-packages/ariba/report.py
/usr/lib/python3/dist-packages/ariba/report_filter.py
/usr/lib/python3/dist-packages/ariba/report_flag_expander.py
/usr/lib/python3/dist-packages/ariba/samtools_variants.py
/usr/lib/python3/dist-packages/ariba/scaffold_graph.py
/usr/lib/python3/dist-packages/ariba/sequence_metadata.py
/usr/lib/python3/dist-packages/ariba/sequence_variant.py
/usr/lib/python3/dist-packages/ariba/summary.py
/usr/lib/python3/dist-packages/ariba/summary_cluster.py
/usr/lib/python3/dist-packages/ariba/summary_cluster_variant.py
/usr/lib/python3/dist-packages/ariba/summary_sample.py
/usr/lib/python3/dist-packages/ariba/tasks/__init__.py
/usr/lib/python3/dist-packages/ariba/tasks/aln2meta.py
/usr/lib/python3/dist-packages/ariba/tasks/expandflag.py
/usr/lib/python3/dist-packages/ariba/tasks/flag.py
/usr/lib/python3/dist-packages/ariba/tasks/getref.py
/usr/lib/python3/dist-packages/ariba/tasks/micplot.py
/usr/lib/python3/dist-packages/ariba/tasks/prepareref.py
/usr/lib/python3/dist-packages/ariba/tasks/prepareref_tb.py
/usr/lib/python3/dist-packages/ariba/tasks/pubmlstget.py
/usr/lib/python3/dist-packages/ariba/tasks/pubmlstspecies.py
/usr/lib/python3/dist-packages/ariba/tasks/refquery.py
/usr/lib/python3/dist-packages/ariba/tasks/reportfilter.py
/usr/lib/python3/dist-packages/ariba/tasks/run.py
/usr/lib/python3/dist-packages/ariba/tasks/summary.py
/usr/lib/python3/dist-packages/ariba/tasks/test.py
/usr/lib/python3/dist-packages/ariba/tasks/version.py
/usr/lib/python3/dist-packages/ariba/tb.py
/usr/lib/python3/dist-packages/ariba/tb_data/NC_000962.3.fa.gz
/usr/lib/python3/dist-packages/ariba/tb_data/NC_000962.3.gb
/usr/lib/python3/dist-packages/ariba/tb_data/panel.20181115.json
/usr/lib/python3/dist-packages/ariba/tb_data/panel.20181115.txt
/usr/lib/python3/dist-packages/ariba/tb_data/panel.20181221.json
/usr/lib/python3/dist-packages/ariba/tb_data/panel.20181221.txt
/usr/lib/python3/dist-packages/ariba/tb_data/panel.20190102.json
/usr/lib/python3/dist-packages/ariba/tb_data/panel.20190102.txt
/usr/lib/python3/dist-packages/ariba/test_run_data/metadata.tsv
/usr/lib/python3/dist-packages/ariba/test_run_data/reads_1.fq
/usr/lib/python3/dist-packages/ariba/test_run_data/reads_2.fq
/usr/lib/python3/dist-packages/ariba/test_run_data/ref_fasta_to_make_reads_from.fa
/usr/lib/python3/dist-packages/ariba/test_run_data/ref_seqs.fa
/usr/lib/python3/dist-packages/ariba/tests/__init__.py
/usr/lib/python3/dist-packages/ariba/tests/aln_to_metadata_test.py
/usr/lib/python3/dist-packages/ariba/tests/assembly_compare_test.py
/usr/lib/python3/dist-packages/ariba/tests/assembly_test.py
/usr/lib/python3/dist-packages/ariba/tests/assembly_variants_test.py
/usr/lib/python3/dist-packages/ariba/tests/bam_parse_test.py
/usr/lib/python3/dist-packages/ariba/tests/card_record_test.py
/usr/lib/python3/dist-packages/ariba/tests/cdhit_test.py
/usr/lib/python3/dist-packages/ariba/tests/cluster_test.py
/usr/lib/python3/dist-packages/ariba/tests/clusters_test.py
/usr/lib/python3/dist-packages/ariba/tests/common_test.py
/usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_load_aln_file.in.fa
/usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_make_cluster_file.out
/usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_coding.in.fa
/usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_coding.in.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_coding.out.cluster
/usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_coding.out.fa
/usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_coding.out.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.in.fa
/usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster
/usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.out.fa
/usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.expected.fa
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.expected.log
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite.expected.fa
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite.expected.log
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite.reads.fq
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite_fail.reads.fq
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite_fails.expected.log
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_check_spades_log_file.log.bad
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_check_spades_log_file.log.good
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_fix_contig_orientation.in.fa
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_fix_contig_orientation.out.fa
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_parse_assembly_bam.bam
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa
/usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps
/usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_parse.bam
/usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_parse.reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_parse.reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_parse.ref.fa
/usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam
/usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq
/usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa
/usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam
/usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq
/usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa
/usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam
/usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa
/usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_best_seq_ref.fa
/usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai
/usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa
/usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai
/usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa
/usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai
/usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_fake_run.in.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in
/usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_load_user_clusters_file.bad1
/usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_load_user_clusters_file.bad2
/usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_load_user_clusters_file.bad3
/usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_load_user_clusters_file.good
/usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_run.in.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters
/usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_count_reads_1.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_count_reads_2.fq
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv
/usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq
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