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();     # => AC12345.6

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 <jac@ncgr.org>

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.

cpanm Bio::SeqReader

perl -MCPAN -e shell
install Bio::SeqReader