class Wgsim::Mutate::Core
- Wgsim::Mutate::Core
- Reference
- Object
Included Modules
Defined in:
wgsim/mutate/core.crConstructors
Instance Method Summary
- #delete_nucleotide(n : UInt8) : RefBase
- #deletion_extension_probability : Float64
- #deletion_extension_probability=(deletion_extension_probability : Float64)
- #deletion_rate : Float64
- #deletion_rate=(deletion_rate : Float64)
-
#generate_insertion : Slice(UInt8)
Generate insertion based on given size and indel extension probability
- #insert_nucleotide(n : UInt8) : RefBase
- #insertion_extension_probability : Float64
- #insertion_extension_probability=(insertion_extension_probability : Float64)
- #insertion_rate : Float64
- #insertion_rate=(insertion_rate : Float64)
- #log_deletion : Nil
- #log_insertion(n, ins) : Nil
- #log_substitution(n, nn) : Nil
- #nochange_nucleotide(n : UInt8) : RefBase
- #rand(*args, **options)
- #rand(*args, **options, &)
- #randn(*args, **options)
- #randn(*args, **options, &)
- #seed : UInt64 | Nil
- #seed=(seed : UInt64 | Nil)
- #simulate_mutations(sequence : Slice(UInt8)) : Tuple(RefSeq, Array(EventRecord))
- #substitute_nucleotide(n : UInt8) : RefBase
- #substitution_rate : Float64
- #substitution_rate=(substitution_rate : Float64)
Instance methods inherited from module Wgsim::CoreUtils
perform_substitution(base : UInt8, i : 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)
#
Instance Method Detail
def generate_insertion : Slice(UInt8)
#
Generate insertion based on given size and indel extension probability