class ActionLowQuality

Author: Almudena Bocinos Rioboo

Defines the main methods that are necessary to execute PluginActionLowHighSize

Inherit: Plugin

Public Class Methods

new(start_pos,end_pos) click to toggle source
Calls superclass method SeqtrimAction::new
# File lib/seqtrimnext/actions/action_low_quality.rb, line 12
def initialize(start_pos,end_pos)
   super(start_pos,end_pos)    
   # esto es cut=false porque al principio el plugin lowqual estaba al inicio del pipeline y habia que dejar
   # la secuencia larga para que se encontrasen los contaminantes y vectores
   # Tambien esta por si un linker tiene baja calidad que pueda encontrarlo
   @cut =false
 end

Public Instance Methods

apply_decoration(char) click to toggle source

def apply_to(seq)

# seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos)
$LOG.debug " Applying #{self.class}  to #{seq.seq_name} . This sequence will be ignored due to low quality " 
#delete sequence if it was created

end

# File lib/seqtrimnext/actions/action_low_quality.rb, line 30
def apply_decoration(char)
  return char.downcase.on_white
end