Class: Read

Inherits:
Object
  • Object
show all
Defined in:
lib/scbi_ace/read.rb

Overview

Description: This class provided the methods to add Reads data —- Author: Noe Fernandez Pozo —— Date: 31-May-2011

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(name, orientation, start_in_consensus) ⇒ Read

Returns a new instance of Read.



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# File 'lib/scbi_ace/read.rb', line 11

def initialize(name,orientation,start_in_consensus)
	@name = name
	@orientation = orientation
	@start_in_consensus = start_in_consensus
	@bs = []
end

Instance Attribute Details

#align_clip_end ⇒ Object

Returns the value of attribute align_clip_end.



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# File 'lib/scbi_ace/read.rb', line 9

def align_clip_end
  @align_clip_end
end

#align_clip_start ⇒ Object

Returns the value of attribute align_clip_start.



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# File 'lib/scbi_ace/read.rb', line 9

def align_clip_start
  @align_clip_start
end

#bs ⇒ Object

Returns the value of attribute bs.



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# File 'lib/scbi_ace/read.rb', line 7

def bs
  @bs
end

#fasta ⇒ Object

Returns the value of attribute fasta.



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# File 'lib/scbi_ace/read.rb', line 7

def fasta
  @fasta
end

#item_num ⇒ Object

Returns the value of attribute item_num.



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# File 'lib/scbi_ace/read.rb', line 8

def item_num
  @item_num
end

#name ⇒ Object

Returns the value of attribute name.



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# File 'lib/scbi_ace/read.rb', line 7

def name
  @name
end

#orientation ⇒ Object

Returns the value of attribute orientation.



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# File 'lib/scbi_ace/read.rb', line 7

def orientation
  @orientation
end

#padded_bases_num ⇒ Object

Returns the value of attribute padded_bases_num.



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# File 'lib/scbi_ace/read.rb', line 8

def padded_bases_num
  @padded_bases_num
end

#qual_clip_end ⇒ Object

Returns the value of attribute qual_clip_end.



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# File 'lib/scbi_ace/read.rb', line 9

def qual_clip_end
  @qual_clip_end
end

#qual_clip_start ⇒ Object

Returns the value of attribute qual_clip_start.



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# File 'lib/scbi_ace/read.rb', line 9

def qual_clip_start
  @qual_clip_start
end

#start_in_consensus ⇒ Object

Returns the value of attribute start_in_consensus.



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# File 'lib/scbi_ace/read.rb', line 7

def start_in_consensus
  @start_in_consensus
end

#tag_num ⇒ Object

Returns the value of attribute tag_num.



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# File 'lib/scbi_ace/read.rb', line 8

def tag_num
  @tag_num
end

Instance Method Details

#add_bs(bs) ⇒ Object 



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# File 'lib/scbi_ace/read.rb', line 35

def add_bs(bs)
	@bs.push bs
end

#add_data(padded_bases_num, item_num, tag_num) ⇒ Object 



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# File 'lib/scbi_ace/read.rb', line 22

def add_data(padded_bases_num,item_num,tag_num)
	@padded_bases_num = padded_bases_num
	@item_num = item_num
	@tag_num = tag_num
end

#add_fasta(fasta) ⇒ Object 



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# File 'lib/scbi_ace/read.rb', line 18

def add_fasta(fasta)
	@fasta = fasta
end

#add_qual_clipping(qual_clip_start, qual_clip_end, align_clip_start, align_clip_end) ⇒ Object 



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# File 'lib/scbi_ace/read.rb', line 28

def add_qual_clipping(qual_clip_start, qual_clip_end, align_clip_start, align_clip_end)
	@qual_clip_start = qual_clip_start
	@qual_clip_end = qual_clip_end
	@align_clip_start = align_clip_start
	@align_clip_end = align_clip_end
end