NAME

Bio::SeqReader::FastqRecord - Class providing methods for representing header, sequence, and quality information in FASTQ records.

SYNOPSIS

   use Bio::SeqReader::FastqRecord;

EXAMPLES

   my $so = new Bio::SeqReader::FastqRecord();
   $so->seq( 'ACGTACGT' );
   print $so->seq();       # ACGTACGT

DESCRIPTION

Class representing a sequence in FASTQ format. Headers 1 and 2, sequence text, and quality text are accessed by the object's getter-setter methods.

CLASS METHODS

Bio::SeqReader::FastqRecord provides no class methods.

INSTANCE METHODS

Bio::SeqReader::FastqRecord provides the following instance methods.

new

Returns a new Bio::SeqReader::FastqRecord object.

 # Void constructor
 my $so = new Bio::SeqReader::FastqRecord();

 # Constructor with initial values
 my $so = new Bio::SeqReader::FastqRecord(
                  header1     => 'R_12345 read info ...',
                  seqtext     => 'ACGTACGT',
                  header2     => '',
                  qualtext    => 'A@AA?#??'
                  );

header1

Getter-setter for the first header text from a Bio::SeqReader::FastqRecord object.

 $so->header1( 'R_12345 read info ...' );
 print $so->header1();     # => R_12345 read info

header2

Getter-setter for the second header text from a Bio::SeqReader::FastqRecord object.

 $so->header2( 'second header info ...' );
 print $so->header2();     # => second header info ...

quals

Getter-setter for the quality text from a Bio::SeqReader::FastqRecord object.

 $so->quals( 'A@AA?#??' );
 print $so->quals();     # => A@AA?#??

reset

Reset a Bio::SeqReader::FastqRecord object.

seq

Getter-setter for the sequence text from a Bio::SeqReader::FastqRecord object.

 $so->seq( 'ACGTACGT' );
 print $so->seq();     # => ACGTACGT

EXTERNAL DEPENDENCIES

Perl core.

EXAMPLES

BUGS

None reported yet, but let me know.

SEE ALSO

Bio::SeqReader::Fastq.

AUTHOR

John A. Crow <crowja@gmail.com>

COPYRIGHT AND LICENSE

  Copyright (C) 2012 by John A. Crow
  Copyright (C) 2012 by National Center for Genome Resources

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.0 or, at your option, any later version of Perl 5 you may have available.