class Wgsim::Sequencing::ReadPairSimulator

Included Modules

Defined in:

wgsim/sequencing/read_pair_simulator.cr

Constant Summary

MAX_INSERT_SIZE_RESAMPLINGS = 10000
PROGRESS_REPORT_COUNT = 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(average_depth : Float64, mean_insert_size : Int32, insert_size_std_dev : Int32, read1_length : Int32, read2_length : Int32, error_rate : Float64, max_ambiguous_ratio : Float64, seed : UInt64 | Nil = nil) #

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Instance Method Detail

def average_depth : Float64 #

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def average_depth=(average_depth : Float64) #

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def build_read_pair_sequences(contig_sequence, fragment_start, insert_size, read1_starts_at_fragment_left : Bool) : Tuple(Slice(UInt8), Slice(UInt8)) #

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def error_rate : Float64 #

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def error_rate=(error_rate : Float64) #

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def insert_size_std_dev : Int32 #

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def insert_size_std_dev=(insert_size_std_dev : Int32) #

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def max_ambiguous_ratio : Float64 #

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def max_ambiguous_ratio=(max_ambiguous_ratio : Float64) #

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def mean_insert_size : Int32 #

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def mean_insert_size=(mean_insert_size : Int32) #

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def next_bool(*args, **options) #

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

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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 read1_length : Int32 #

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def read1_length=(read1_length : Int32) #

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def read2_length : Int32 #

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def read2_length=(read2_length : Int32) #

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def sample_fragment_start(contig_length : Int, insert_size : Int) : Int32 #

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def sample_insert_size(contig_length : Int32) : Int32 #

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def simulate_read_pairs(sequence_name, sequence, &) #

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