Index

A

accuracy (alignparse.ccs.Summary attribute) add_mut_info_cols() (in module alignparse.consensus) align() (alignparse.targets.Targets method) align_and_parse() (alignparse.targets.Targets method) Alignment (class in alignparse.cs_tag) alignparse module alignparse.ccs module alignparse.consensus module

alignparse.constants module alignparse.cs_tag module alignparse.minimap2 module alignparse.targets module alignparse.utils module

C

CBPALETTE (in module alignparse.constants) ccs_stats() (alignparse.ccs.Summaries method) cs (alignparse.cs_tag.Alignment attribute) cs_introns_to_deletions() (in module alignparse.cs_tag) cs_op_len_target() (in module alignparse.cs_tag)

cs_op_type() (in module alignparse.cs_tag) cs_to_mutation_str() (in module alignparse.cs_tag) cs_to_nt_mutation_count() (in module alignparse.cs_tag) cs_to_op_mutation_count() (in module alignparse.cs_tag) cs_to_sequence() (in module alignparse.cs_tag)

D

deletions (alignparse.consensus.Mutations attribute)

dels_to_subs() (alignparse.utils.InFrameDeletionsToSubs method)

E

empirical_accuracy() (in module alignparse.consensus)

end (alignparse.targets.Feature attribute) extract_cs() (alignparse.cs_tag.Alignment method)

F

fastqfile (alignparse.ccs.Summary attribute) Feature (class in alignparse.targets) feature_names (alignparse.targets.Target attribute)

feature_parse_specs() (alignparse.targets.Targets method) features (alignparse.targets.Target attribute) features_to_parse() (alignparse.targets.Targets method)

G

geneseq (alignparse.utils.InFrameDeletionsToSubs attribute) get_accuracy() (alignparse.cs_tag.Alignment method) get_ccs_stats() (in module alignparse.ccs)

get_feature() (alignparse.targets.Target method) get_name() (alignparse.targets.Target class method) get_target() (alignparse.targets.Targets method)

H

has_feature() (alignparse.targets.Target method)

has_stat() (alignparse.ccs.Summaries method) has_zmw_stats() (alignparse.ccs.Summaries method)

I

image() (alignparse.targets.Target method)

InFrameDeletionsToSubs (class in alignparse.utils) insertions (alignparse.consensus.Mutations attribute)

L

length (alignparse.ccs.Summary attribute) (alignparse.targets.Feature attribute) (alignparse.targets.Target attribute)

M

map_to_sam() (alignparse.minimap2.Mapper method) Mapper (class in alignparse.minimap2) merge_dels() (in module alignparse.utils) module alignparse alignparse.ccs alignparse.consensus alignparse.constants alignparse.cs_tag alignparse.minimap2 alignparse.targets alignparse.utils

MutationRenumber (class in alignparse.utils) Mutations (class in alignparse.consensus)

N

name (alignparse.ccs.Summary attribute) (alignparse.targets.Feature attribute) (alignparse.targets.Target attribute)

O

old_to_new_site (alignparse.utils.MutationRenumber attribute) old_to_wt (alignparse.utils.MutationRenumber attribute) options (alignparse.minimap2.Mapper attribute)

OPTIONS_CODON_DMS (in module alignparse.minimap2) OPTIONS_VIRUS_W_DEL (in module alignparse.minimap2) orientation (alignparse.cs_tag.Alignment attribute)

P

parse_alignment() (alignparse.targets.Targets method) passes (alignparse.ccs.Summary attribute) plot() (alignparse.targets.Targets method)

plot_ccs_stats() (alignparse.ccs.Summaries method) plot_zmw_stats() (alignparse.ccs.Summaries method) process_mut_str() (in module alignparse.consensus) prog (alignparse.minimap2.Mapper attribute)

Q

query_clip3 (alignparse.cs_tag.Alignment attribute) query_clip5 (alignparse.cs_tag.Alignment attribute)

query_name (alignparse.cs_tag.Alignment attribute) qvals_to_accuracy() (in module alignparse.utils)

R

renumber_muts() (alignparse.utils.MutationRenumber method) report_to_stats() (in module alignparse.ccs)

reportfile (alignparse.ccs.Summary attribute) retain_tags (alignparse.minimap2.Mapper attribute)

S

seq (alignparse.targets.Feature attribute) (alignparse.targets.Target attribute) shiftable() (alignparse.utils.InFrameDeletionsToSubs method) simple_mutconsensus() (in module alignparse.consensus) sort_mutations() (in module alignparse.utils)

split_cs() (in module alignparse.cs_tag) start (alignparse.targets.Feature attribute) substitutions (alignparse.consensus.Mutations attribute) summaries (alignparse.ccs.Summaries attribute) Summaries (class in alignparse.ccs) Summary (class in alignparse.ccs)

T

Target (class in alignparse.targets) target_clip5 (alignparse.cs_tag.Alignment attribute) target_lastpos (alignparse.cs_tag.Alignment attribute) target_name (alignparse.cs_tag.Alignment attribute)

target_names (alignparse.targets.Targets attribute) target_seqs (alignparse.targets.Targets attribute) targets (alignparse.targets.Targets attribute) Targets (class in alignparse.targets)

V

version (alignparse.minimap2.Mapper attribute)

W

write_fasta() (alignparse.targets.Targets method)

Z

zmw_stats (alignparse.ccs.Summary attribute)

zmw_stats() (alignparse.ccs.Summaries method)