class Wgsim::Mutate::MutationSimulator

Included Modules

Defined in:

wgsim/mutate/mutation_simulator.cr

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(substitution_rate : Float64, insertion_rate : Float64, deletion_rate : Float64, insertion_extension_probability : Float64, deletion_extension_probability : Float64, seed : UInt64 | Nil = nil) #

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Instance Method Detail

def build_deleted_reference_base(reference_base : UInt8, deleted_bases : Array(UInt8)) : ReferenceBase #

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def build_insertion_reference_base(reference_base : UInt8, mutation_events : Array(MutationEvent), reference_position : Int32) : ReferenceBase #

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def build_substituted_reference_base(reference_base : UInt8, mutation_events : Array(MutationEvent), reference_position : Int32) : ReferenceBase #

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def build_unchanged_reference_base(reference_base : UInt8) : ReferenceBase #

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def deletion_extension_probability : Float64 #

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def deletion_extension_probability=(deletion_extension_probability : Float64) #

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def deletion_rate : Float64 #

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def deletion_rate=(deletion_rate : Float64) #

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def generate_inserted_bases : Slice(UInt8) #

Generate inserted bases based on the insertion extension probability.


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def insertion_extension_probability : Float64 #

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def insertion_extension_probability=(insertion_extension_probability : Float64) #

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def insertion_rate : Float64 #

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def insertion_rate=(insertion_rate : Float64) #

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def rand(*args, **options) #

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def rand(*args, **options, &) #

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def randn(*args, **options) #

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def randn(*args, **options, &) #

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def seed : UInt64 | Nil #

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def seed=(seed : UInt64 | Nil) #

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def simulate_mutations(sequence : Slice(UInt8)) : Tuple(ReferenceSequence, Array(MutationEvent)) #

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def substitution_rate : Float64 #

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def substitution_rate=(substitution_rate : Float64) #

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