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?#??'
                  );

display_id()

Getter for the display id associated with a Bio::SeqReader::FastqRecord object. Makes use of the current contents of header 1.

  print $so->display_id();   # => R_12345 

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. Basically sets all internal data to empty strings.

seq()

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

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

EXTERNAL DEPENDENCIES

Perl core.

BUGS

None reported yet, but let me know.

SEE ALSO

Bio::SeqReader::Fastq, Bio::SeqReader.

AUTHOR

John A. Crow <jac_at_cpan_dot_org>

COPYRIGHT AND LICENSE

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.

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