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