class Wgsim::Sequencing::ErrorModel

Overview

A simple sequencing-error model.

This class represents observation errors made by the sequencer, not biological mutations in the genome. It only substitutes A/C/G/T bases; ambiguous N bases remain N because their true base is unknown.

Included Modules

Defined in:

wgsim/sequencing/error_model.cr

Constant Summary

PHRED_ASCII_OFFSET = 33
PHRED_SCORE_FACTOR = -10

Constructors

Instance Method Summary

Instance methods inherited from module Wgsim::Dna

normalize_base(base : UInt8) : UInt8 normalize_base, normalize_sequence(sequence : Slice(UInt8)) : Slice(UInt8) normalize_sequence, perform_substitution(base : UInt8, substitution_index : Int) : UInt8 perform_substitution, reverse_complement(sequence : Slice(UInt8)) : Slice(UInt8) reverse_complement

Constructor Detail

def self.new(error_rate : Float64, random : Rand) #

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Instance Method Detail

def add_errors(sequence : Slice(UInt8)) : Slice(UInt8) #

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def quality_char : Char #

FASTQ qualities encode error probability as an ASCII character. Here we use one uniform quality character for every base in a read.


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