class Depth::Core::CoverageCalculator

Included Modules

Defined in:

depth/core/coverage_calculator.cr

Constructors

Instance Method Summary

Instance methods inherited from module Depth::Core::Cigar

cigar_each_event(cigar, ipos : Int32, & : Int32, Int32 -> ) cigar_each_event, cigar_each_segment(cigar, ipos : Int32, & : Tuple(Int32, Int32) -> ) cigar_each_segment, cigar_fill_events!(cigar, ipos : Int32, evbuf : Array(Tuple(Int32, Int32))) : Nil cigar_fill_events!, cigar_segments(cigar, ipos : Int32) : Array(Tuple(Int32, Int32)) cigar_segments, cigar_start_end_events(cigar, ipos : Int32) : Array(Tuple(Int32, Int32)) cigar_start_end_events, inc_coverage(cigar, ipos : Int32, a : Coverage) inc_coverage

Constructor Detail

def self.new(bam : HTS::Bam, options : Options) #

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Instance Method Detail

def calculate(a : Coverage, r : Region | Nil, offset : Int32 = 0) : Int32 #

Returns: CoverageResult enum values or tid


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def initialize_coverage_array(coverage : Coverage, chrom_len : Int32) #

Initialize coverage array for a chromosome


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def reset_coverage!(a : Coverage, limit : Int32) #

Reset using touch marks: zero only indices written in current generation (up to limit)


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