class Mpileup
Public Class Methods
new(file_path)
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# File lib/full_lengther_next/mapping.rb, line 4 def initialize(file_path) @mpileup_file = ScbiZcatFile.new(file_path) @last_line = nil end
Public Instance Methods
close()
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# File lib/full_lengther_next/mapping.rb, line 51 def close @mpileup_file.close end
initialize_contig(contig_length)
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# File lib/full_lengther_next/mapping.rb, line 45 def initialize_contig(contig_length) coverages = Array.new(contig_length, 0) coverages[@last_line[1].to_i-1] = @last_line[2].to_i return coverages end
read_contig(contig_name, contig_length)
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# File lib/full_lengther_next/mapping.rb, line 9 def read_contig(contig_name, contig_length) coverages = [] if !@last_line.nil? if @last_line[0] != contig_name return nil else coverages = initialize_contig(contig_length) end else line = @mpileup_file.readline if line.nil? @last_line = nil return nil else @last_line = line.chomp.split("\t") if @last_line[0] != contig_name return nil else coverages = initialize_contig(contig_length) end end end while !@mpileup_file.eof fields = @mpileup_file.readline.chomp.split("\t") contig = fields[0] if contig == contig_name coverages[fields[1].to_i-1] = fields[2].to_i else @last_line = fields break end end return coverages end