Index

A

alphabet (bioquik.FMIndex attribute) (bioquik.fmindex.FMIndex attribute) (bioquik.WaveletTree attribute) (bioquik.wavelettree.WaveletTree attribute)

B

bioquik module bioquik.cli module bioquik.fasta_worker module bioquik.fmindex module bioquik.motifs module bioquik.plotter module bioquik.processor module

bioquik.reports module bioquik.validate module bioquik.wavelettree module bitvec (bioquik.WaveletTree attribute) (bioquik.wavelettree.WaveletTree attribute) build_pattern_to_motifs() (in module bioquik) (in module bioquik.motifs) bwt (bioquik.FMIndex attribute) (bioquik.fmindex.FMIndex attribute)

C

C (bioquik.FMIndex attribute) (bioquik.fmindex.FMIndex attribute) combine_csv() (in module bioquik.reports)

count() (bioquik.FMIndex method) (bioquik.fmindex.FMIndex method) (in module bioquik.cli)

F

FMIndex (class in bioquik) (class in bioquik.fmindex)

G

generate_motifs() (in module bioquik) (in module bioquik.motifs)

L

left (bioquik.WaveletTree attribute) (bioquik.wavelettree.WaveletTree attribute) length (bioquik.WaveletTree attribute) (bioquik.wavelettree.WaveletTree attribute)

locate() (bioquik.FMIndex method) (bioquik.fmindex.FMIndex method)

M

module bioquik bioquik.cli bioquik.fasta_worker bioquik.fmindex bioquik.motifs bioquik.plotter bioquik.processor bioquik.reports bioquik.validate bioquik.wavelettree

P

plot_distribution() (in module bioquik.plotter) plot_heatmap() (in module bioquik.plotter) prefix_ranks (bioquik.WaveletTree attribute) (bioquik.wavelettree.WaveletTree attribute)

process_fasta_file() (in module bioquik) (in module bioquik.fasta_worker)

R

rank() (bioquik.WaveletTree method) (bioquik.wavelettree.WaveletTree method)

right (bioquik.WaveletTree attribute) (bioquik.wavelettree.WaveletTree attribute) run_count() (in module bioquik.processor)

S

sa_sample_rate (bioquik.FMIndex attribute) (bioquik.fmindex.FMIndex attribute) sa_samples (bioquik.FMIndex attribute) (bioquik.fmindex.FMIndex attribute) sample_rate (bioquik.WaveletTree attribute) (bioquik.wavelettree.WaveletTree attribute)

seq (bioquik.FMIndex attribute) (bioquik.fmindex.FMIndex attribute) seq_b (bioquik.FMIndex attribute) (bioquik.fmindex.FMIndex attribute)

V

validate_dir() (in module bioquik.validate)

validate_patterns() (in module bioquik.validate)

W

WaveletTree (class in bioquik) (class in bioquik.wavelettree)

write_summary() (in module bioquik.reports) wt (bioquik.FMIndex attribute) (bioquik.fmindex.FMIndex attribute)