AUTHORS
LICENSE
MANIFEST.in
README.md
setup.py
ariba/__init__.py
ariba/aln_to_metadata.py
ariba/assembly.py
ariba/assembly_compare.py
ariba/assembly_variants.py
ariba/bam_parse.py
ariba/card_record.py
ariba/cdhit.py
ariba/cluster.py
ariba/clusters.py
ariba/common.py
ariba/external_progs.py
ariba/faidx.py
ariba/flag.py
ariba/histogram.py
ariba/link.py
ariba/mapping.py
ariba/megares_data_finder.py
ariba/megares_zip_parser.py
ariba/mic_plotter.py
ariba/mlst_profile.py
ariba/mlst_reporter.py
ariba/pubmlst_getter.py
ariba/pubmlst_ref_preparer.py
ariba/read_filter.py
ariba/read_store.py
ariba/ref_genes_getter.py
ariba/ref_preparer.py
ariba/ref_seq_chooser.py
ariba/refdata_query.py
ariba/reference_data.py
ariba/report.py
ariba/report_filter.py
ariba/report_flag_expander.py
ariba/samtools_variants.py
ariba/scaffold_graph.py
ariba/sequence_metadata.py
ariba/sequence_variant.py
ariba/summary.py
ariba/summary_cluster.py
ariba/summary_cluster_variant.py
ariba/summary_sample.py
ariba/tb.py
ariba/versions.py
ariba/vfdb_parser.py
ariba.egg-info/PKG-INFO
ariba.egg-info/SOURCES.txt
ariba.egg-info/dependency_links.txt
ariba.egg-info/requires.txt
ariba.egg-info/top_level.txt
ariba/ext/fml-asm_ariba.cpp
ariba/ext/minimap_ariba.cpp
ariba/ext/vcfcall_ariba.cpp
ariba/tasks/__init__.py
ariba/tasks/aln2meta.py
ariba/tasks/expandflag.py
ariba/tasks/flag.py
ariba/tasks/getref.py
ariba/tasks/micplot.py
ariba/tasks/prepareref.py
ariba/tasks/prepareref_tb.py
ariba/tasks/pubmlstget.py
ariba/tasks/pubmlstspecies.py
ariba/tasks/refquery.py
ariba/tasks/reportfilter.py
ariba/tasks/run.py
ariba/tasks/summary.py
ariba/tasks/test.py
ariba/tasks/version.py
ariba/tb_data/NC_000962.3.fa.gz
ariba/tb_data/NC_000962.3.gb
ariba/tb_data/panel.20181115.json
ariba/tb_data/panel.20181115.txt
ariba/tb_data/panel.20181221.json
ariba/tb_data/panel.20181221.txt
ariba/tb_data/panel.20190102.json
ariba/tb_data/panel.20190102.txt
ariba/test_run_data/metadata.tsv
ariba/test_run_data/reads_1.fq
ariba/test_run_data/reads_2.fq
ariba/test_run_data/ref_fasta_to_make_reads_from.fa
ariba/test_run_data/ref_seqs.fa
ariba/tests/__init__.py
ariba/tests/aln_to_metadata_test.py
ariba/tests/assembly_compare_test.py
ariba/tests/assembly_test.py
ariba/tests/assembly_variants_test.py
ariba/tests/bam_parse_test.py
ariba/tests/card_record_test.py
ariba/tests/cdhit_test.py
ariba/tests/cluster_test.py
ariba/tests/clusters_test.py
ariba/tests/common_test.py
ariba/tests/external_progs_test.py
ariba/tests/faidx_test.py
ariba/tests/flag_test.py
ariba/tests/histogram_test.py
ariba/tests/link_test.py
ariba/tests/mapping_test.py
ariba/tests/megares_data_finder_test.py
ariba/tests/megares_zip_parser_test.py
ariba/tests/mic_plotter_test.py
ariba/tests/mlst_profile_test.py
ariba/tests/mlst_reporter_test.py
ariba/tests/ncbi_getter_test.py
ariba/tests/pubmlst_getter_test.py
ariba/tests/pubmlst_ref_preparer_test.py
ariba/tests/read_filter_test.py
ariba/tests/read_store_test.py
ariba/tests/ref_genes_getter_test.py
ariba/tests/ref_preparer_test.py
ariba/tests/ref_seq_chooser_test.py
ariba/tests/reference_data_test.py
ariba/tests/report_filter_test.py
ariba/tests/report_flag_expander_test.py
ariba/tests/samtools_variants_test.py
ariba/tests/scaffold_graph_test.py
ariba/tests/sequence_metadata_test.py
ariba/tests/sequence_variant_test.py
ariba/tests/summary_cluster_test.py
ariba/tests/summary_cluster_variant_test.py
ariba/tests/summary_sample_test.py
ariba/tests/summary_test.py
ariba/tests/tb_test.py
ariba/tests/test_refdata_query.py
ariba/tests/versions_test.py
ariba/tests/vfdb_parser_test.py
scripts/ariba
third_party/fermi-lite-0.1/bfc.c
third_party/fermi-lite-0.1/bseq.c
third_party/fermi-lite-0.1/bubble.c
third_party/fermi-lite-0.1/fml.h
third_party/fermi-lite-0.1/htab.c
third_party/fermi-lite-0.1/htab.h
third_party/fermi-lite-0.1/internal.h
third_party/fermi-lite-0.1/khash.h
third_party/fermi-lite-0.1/kmer.h
third_party/fermi-lite-0.1/kseq.h
third_party/fermi-lite-0.1/ksort.h
third_party/fermi-lite-0.1/kstring.h
third_party/fermi-lite-0.1/ksw.c
third_party/fermi-lite-0.1/ksw.h
third_party/fermi-lite-0.1/kthread.c
third_party/fermi-lite-0.1/kvec.h
third_party/fermi-lite-0.1/mag.c
third_party/fermi-lite-0.1/mag.h
third_party/fermi-lite-0.1/misc.c
third_party/fermi-lite-0.1/mrope.c
third_party/fermi-lite-0.1/mrope.h
third_party/fermi-lite-0.1/rld0.c
third_party/fermi-lite-0.1/rld0.h
third_party/fermi-lite-0.1/rle.c
third_party/fermi-lite-0.1/rle.h
third_party/fermi-lite-0.1/rope.c
third_party/fermi-lite-0.1/rope.h
third_party/fermi-lite-0.1/unitig.c
third_party/minimap-0.2/bseq.c
third_party/minimap-0.2/bseq.h
third_party/minimap-0.2/index.c
third_party/minimap-0.2/kdq.h
third_party/minimap-0.2/khash.h
third_party/minimap-0.2/kseq.h
third_party/minimap-0.2/ksort.h
third_party/minimap-0.2/kthread.c
third_party/minimap-0.2/kvec.h
third_party/minimap-0.2/map.c
third_party/minimap-0.2/minimap.h
third_party/minimap-0.2/misc.c
third_party/minimap-0.2/sdust.c
third_party/minimap-0.2/sdust.h
third_party/minimap-0.2/sketch.c