class Cominer

Attributes

entropy_function[RW]
freq_table[RW]
position_table[RW]
regions[RW]
single_points[RW]
snps[RW]

Public Class Methods

new(contig) click to toggle source
# File lib/scbi_cominer/cominer.rb, line 10
def initialize(contig)
  
  @freq_table = FrequencyTable.new

      contig.reads.each do |name,read|
    # puts ">#{read.name} #{read.orientation} #{read.align_clip_start} #{read.align_clip_end} #{read.start_in_consensus}"
    # puts read.fasta[read.align_clip_start.to_i..read.align_clip_end.to_i]
    # puts read.fasta
              @freq_table.add_read(read)
      end
      
  # puts freq_table.inspect
  #     exit
  #
      @entropy_function = EntropyFunction.new(@freq_table)
 
  @regions=@entropy_function.regions
  @snps=@entropy_function.snps
  @single_points=@entropy_function.single_points
  
  @freq_table.position_table.delete('-')
  
              @position_table = @freq_table.position_table
              
  
end