Class: Bio::Faster

Inherits:
Object
  • Object
show all
Extended by:
FFI::Library
Defined in:
lib/bio/faster.rb,
lib/bio/faster/library.rb

Defined Under Namespace

Classes: FastQRecord, Library

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(file, encoding = :sanger) ⇒ Faster

Returns a new instance of Faster.



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# File 'lib/bio/faster.rb', line 16

def initialize(file, encoding = :sanger)
    self.file = file
    self.encoding = encoding
end

Instance Attribute Details

#encoding ⇒ Object

Returns the value of attribute encoding.



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# File 'lib/bio/faster.rb', line 15

def encoding
  @encoding
end

#file ⇒ Object

Returns the value of attribute file.



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# File 'lib/bio/faster.rb', line 14

def file
  @file
end

Instance Method Details

#each_record ⇒ Object 



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# File 'lib/bio/faster.rb', line 35

def each_record
    if self.file == :stdin
      self.file = "stdin"
    elsif !File.exists? self.file
      raise ArgumentError, "File #{self.file} does not exist"
    end
    record = FastQRecord.new
    scale_factor = nil
    case self.encoding
      when :sanger then scale_factor = 33
      when :solexa then scale_factor = 64
    end
    record[:filename] = FFI::MemoryPointer.from_string self.file
    while (result = Bio::Faster.fastQ_iterator(record,scale_factor)) == 1
      yield [record[:id].read_string,record[:seq].read_string,record[:quality].read_array_of_int(record[:raw_quality].read_string.length)]
    end
    case result
      when -1 then raise RuntimeError, "Bad formatted FastQ file!"
      when -2 then raise RuntimeError, "Sequence or quality is truncated!"
    end


end