class ActionPairedReads

Author: Almudena Bocinos Rioboo

Defines the main methods that are necessary to execute PluginPairedReads

Inherit: Plugin

Public Class Methods

new(start_pos,end_pos) click to toggle source
Calls superclass method SeqtrimAction::new
# File lib/seqtrimnext/actions/action_paired_reads.rb, line 10
def initialize(start_pos,end_pos)
   super(start_pos,end_pos)    
   @cut =true

 end

Public Instance Methods

apply_to(seq) click to toggle source
# File lib/seqtrimnext/actions/action_paired_reads.rb, line 17
def apply_to(seq)
  $LOG.debug "Applying #{self.class}"
  
  #Storage the first and second subsequences
  subseq1 = seq.seq_fasta[0,@start_pos-1]        
  subseq2 = seq.seq_fasta[@end_pos+1,seq.seq_fasta.length-1]
  #$LOG.debug "\nSubsequence left: #{subseq1} \n Subsequence right: #{subseq2}}"

end