Index

_

__init__() (tombo.tombo_helper.Fasta method) (tombo.tombo_helper.intervalData method) (tombo.tombo_helper.TomboMotif method) (tombo.tombo_helper.TomboReads method) (tombo.tombo_stats.AltModel method) (tombo.tombo_stats.ModelStats method) (tombo.tombo_stats.PerReadStats method) (tombo.tombo_stats.TomboModel method)

A

add_read_data() (tombo.tombo_helper.TomboReads method) add_reads() (tombo.tombo_helper.intervalData method)

add_seq() (tombo.tombo_helper.intervalData method) alignInfo (class in tombo.tombo_helper) AltModel (class in tombo.tombo_stats)

C

calc_kmer_fitted_shift_scale() (in module tombo.tombo_stats) close() (tombo.tombo_stats.ModelStats method) (tombo.tombo_stats.PerReadStats method) compute_base_means() (in module tombo.tombo_stats) compute_ctrl_motif_stats() (tombo.tombo_stats.ModelStats method) (tombo.tombo_stats.PerReadStats method)

compute_ground_truth_stats() (tombo.tombo_stats.ModelStats method) (tombo.tombo_stats.PerReadStats method) compute_motif_stats() (tombo.tombo_stats.ModelStats method) (tombo.tombo_stats.PerReadStats method) compute_num_events() (in module tombo.tombo_stats) copy() (tombo.tombo_helper.intervalData method)

D

dpResults (class in tombo.tombo_helper)

E

expand_interval() (tombo.tombo_helper.intervalData method)

F

Fasta (class in tombo.tombo_helper) find_adaptive_base_assignment() (in module tombo.resquiggle)

find_mod_poss() (tombo.tombo_helper.TomboMotif method) find_seq_start_in_events() (in module tombo.resquiggle) find_static_base_assignment() (in module tombo.resquiggle)

G

genomeLocation (class in tombo.tombo_helper) get_all_cs() (tombo.tombo_helper.TomboReads method) get_base_levels() (tombo.tombo_helper.intervalData method) get_coverage() (tombo.tombo_helper.TomboReads method) get_cs_coverage() (tombo.tombo_helper.TomboReads method) get_cs_reads() (tombo.tombo_helper.TomboReads method) get_exp_level() (tombo.tombo_stats.AltModel method) get_exp_levels_from_kmers() (tombo.tombo_stats.AltModel method) (tombo.tombo_stats.TomboModel method) get_exp_levels_from_seq() (tombo.tombo_stats.TomboModel method) get_exp_levels_from_seq_with_gaps() (tombo.tombo_stats.TomboModel method) get_exp_sd() (tombo.tombo_stats.AltModel method)

get_most_signif_regions() (tombo.tombo_stats.ModelStats method) get_multiple_slots_read_centric() (in module tombo.tombo_helper) get_pos_stat() (tombo.tombo_stats.ModelStats method) get_raw_read_slot() (in module tombo.tombo_helper) get_read_seg_score() (in module tombo.tombo_stats) get_read_seq() (in module tombo.resquiggle) get_reg_stats() (tombo.tombo_stats.ModelStats method) (tombo.tombo_stats.PerReadStats method) get_region_per_read_stats() (tombo.tombo_stats.PerReadStats method) get_seq() (tombo.tombo_helper.Fasta method) get_seq_sample_type() (in module tombo.tombo_helper) get_single_slot_read_centric() (in module tombo.tombo_helper)

I

intervalData (class in tombo.tombo_helper) is_empty() (tombo.tombo_helper.TomboReads method) is_palindrome (tombo.tombo_helper.TomboMotif attribute) iter_chrms() (tombo.tombo_helper.Fasta method) iter_cov_regs() (tombo.tombo_helper.TomboReads method)

iter_coverage_regions() (tombo.tombo_helper.TomboReads method) iter_cs_coverage() (tombo.tombo_helper.TomboReads method) iter_most_signif_sites() (tombo.tombo_stats.ModelStats method) iter_reads() (tombo.tombo_helper.TomboReads method) iter_stat_seqs() (tombo.tombo_stats.ModelStats method)

L

LevelStats (class in tombo.tombo_stats)

load_resquiggle_parameters() (in module tombo.tombo_stats)

M

map_read() (in module tombo.resquiggle) matches_seq() (tombo.tombo_helper.TomboMotif method) merge() (tombo.tombo_helper.intervalData method) mod_base (tombo.tombo_helper.TomboMotif attribute) mod_pos (tombo.tombo_helper.TomboMotif attribute) ModelStats (class in tombo.tombo_stats)

module tombo tombo.resquiggle tombo.tombo_helper tombo.tombo_stats motif_len (tombo.tombo_helper.TomboMotif attribute) motif_pat (tombo.tombo_helper.TomboMotif attribute)

N

next() (tombo.tombo_helper.TomboReads method) (tombo.tombo_stats.ModelStats method) (tombo.tombo_stats.PerReadStats method)

normalize_raw_signal() (in module tombo.tombo_stats)

P

parse_motif_descs() (in module tombo.tombo_helper)

PerReadStats (class in tombo.tombo_stats)

R

raw_motif (tombo.tombo_helper.TomboMotif attribute) readData (class in tombo.tombo_helper) replace_index() (tombo.tombo_helper.TomboReads method) resolve_skipped_bases_with_raw() (in module tombo.resquiggle)

resquiggle_read() (in module tombo.resquiggle) resquiggleParams (class in tombo.tombo_helper) resquiggleResults (class in tombo.tombo_helper) rev_comp_pat (tombo.tombo_helper.TomboMotif attribute) reverse_sequence_copy() (tombo.tombo_stats.TomboModel method)

S

scaleValues (class in tombo.tombo_helper) segment_signal() (in module tombo.resquiggle)

seqSampleType (class in tombo.tombo_helper) sequenceData (class in tombo.tombo_helper) startClipParams (class in tombo.tombo_helper)

T

tombo module tombo.resquiggle module tombo.tombo_helper module

tombo.tombo_stats module TomboModel (class in tombo.tombo_stats) TomboMotif (class in tombo.tombo_helper) TomboReads (class in tombo.tombo_helper) TomboStats() (in module tombo.tombo_stats)

U

update() (tombo.tombo_helper.intervalData method)

W

write_index_file() (tombo.tombo_helper.TomboReads method)

write_model() (tombo.tombo_stats.AltModel method) (tombo.tombo_stats.TomboModel method)