NAME

       Bio::SeqIO::qual - .qual file input/output stream

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::SeqIO class (see Bio::SeqIO for details).

         my $in_qual = Bio::SeqIO->new(-file    => $qualfile,
                                       -format  => 'qual',
                                       -width   => $width,
                                       -verbose => $verbose);

DESCRIPTION

       This object can transform .qual (similar to fasta) objects to and from Bio::Seq::Quality objects. See
       Bio::Seq::Quality for details.

       Like the fasta module, it can take an argument '-width' to change the number of values per line (defaults
       to 50).

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments
       and suggestions preferably to one of the Bioperl mailing lists.  Your participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look
       at the problem and quickly address it. Please include a thorough description of the problem with code and
       data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.  Bug
       reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR Chad Matsalla

       Chad Matsalla bioinformatics@dieselwurks.com

CONTRIBUTORS

       Jason Stajich, jason@bioperl.org

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded
       with a _

   next_seq()
        Title   : next_seq()
        Usage   : $scf = $stream->next_seq()
        Function: returns the next scf sequence in the stream
        Returns : Bio::Seq::PrimaryQual object
        Notes   : Get the next quality sequence from the stream.

   _next_qual
        Title   : _next_qual
        Usage   : $seq = $stream->_next_qual() (but do not do
                 that. Use $stream->next_seq() instead)
        Function: returns the next quality in the stream
        Returns : Bio::Seq::PrimaryQual object
        Args    : NONE
        Notes  : An internal method. Gets the next quality in
                       the stream.

   next_primary_qual()
        Title   : next_primary_qual()
        Usage   : $seq = $stream->next_primary_qual()
        Function: returns the next sequence in the stream
        Returns : Bio::PrimaryQual object
        Args    : NONE

   width
        Title   : width
        Usage   : $obj->width($newval)
        Function: Get/Set the number of values per line  for FASTA-like output
        Returns : value of width
        Args    : newvalue (optional)

   write_seq
        Title   : write_seq
        Usage   : $obj->write_seq( -source => $source,
                                   -header  => "some information"
                                   -oneline => 0);
        Function: Write out a list of quality values to a fasta-style file.
        Returns : Nothing.
        Args    : Requires a reference to a Bio::Seq::Quality object or a
                  PrimaryQual object as the -source. Option 1: information
                  for the header. Option 2: whether the quality score should
                  be on a single line or not
        Notes   : If no -header is provided, $obj->id() will be used where
                  $obj is a reference to either a Quality object or a
                  PrimaryQual object. If $source->id() fails, "unknown" will
                  be the header. If the Quality object has $source->length()
                  of "DIFFERENT" (read the pod, luke), write_seq will use the
                  length of the PrimaryQual object within the Quality object.