Class: Bio::DB::PileupIterator::PileupRead

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/db/pileup_iterator.rb

Constant Summary collapse

FORWARD_DIRECTION =

Directions relative to reference

'+'
REVERSE_DIRECTION = 
'-'

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ PileupRead

Returns a new instance of PileupRead.



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# File 'lib/bio/db/pileup_iterator.rb', line 155

def initialize
  @sequence = ''
  @insertions = {}
end

Instance Attribute Details

#direction ⇒ Object

sequence is always in the direction of the start of the reference to the end - only @direction gives direction information



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# File 'lib/bio/db/pileup_iterator.rb', line 150

def direction
  @direction
end

#insertions ⇒ Object (readonly)

A hash of recorded insertions. Key of hash is the position in the consensus that is has been added to in the alignment, value is the bases that have been inserted



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# File 'lib/bio/db/pileup_iterator.rb', line 153

def insertions
  @insertions
end

#sequence ⇒ Object

sequence is always in the direction of the start of the reference to the end - only @direction gives direction information



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# File 'lib/bio/db/pileup_iterator.rb', line 150

def sequence
  @sequence
end

Instance Method Details

#add_insertion(position, insertion_length, insertion_bases) ⇒ Object 



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# File 'lib/bio/db/pileup_iterator.rb', line 164

def add_insertion(position, insertion_length, insertion_bases)
  insertions[position] = insertion_bases
end

#read ⇒ Object 



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# File 'lib/bio/db/pileup_iterator.rb', line 160

def read
  @sequence[@sequence.length-2..@sequence.length-1]
end