Class: ActionLowQuality

Inherits:
SeqtrimAction show all
Defined in:
lib/seqtrimnext/actions/action_low_quality.rb

Overview

Author: Almudena Bocinos Rioboo

Defines the main methods that are necessary to execute PluginActionLowHighSize

Inherit: Plugin

Instance Attribute Summary

Attributes inherited from SeqtrimAction

#cut, #end_pos, #found_definition, #informative, #left_action, #message, #reversed, #right_action, #start_pos, #tag_id

Instance Method Summary collapse

Methods inherited from SeqtrimAction

#action_type, #apply_to, #contains?, #contains_action?, #decorate, #description, #inspect, #left_action?, #near_left?, #right_action?, #title, #to_hash, #to_human, #type

Constructor Details

#initialize(start_pos, end_pos) ⇒ ActionLowQuality

Returns a new instance of ActionLowQuality.



12
13
14
15
16
17
18
 
# 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

Instance Method Details

#apply_decoration(char) ⇒ Object 



30
31
32
 
# File 'lib/seqtrimnext/actions/action_low_quality.rb', line 30

def apply_decoration(char)
  return char.downcase.on_white
end