MANIFEST.in
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/best_seq_chooser.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/mash.py
ariba/read_filter.py
ariba/read_store.py
ariba/ref_genes_getter.py
ariba/ref_preparer.py
ariba/refdata_query.py
ariba/reference_data.py
ariba/report.py
ariba/report_filter.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/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/tasks/__init__.py
ariba/tasks/aln2meta.py
ariba/tasks/flag.py
ariba/tasks/getref.py
ariba/tasks/prepareref.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/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
scripts/ariba
scripts/fermilite_ariba.cpython-33m.so
scripts/minimap_ariba.cpython-33m.so
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