NAME

       Bio::SeqIO::phd - phd file input/output stream

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::SeqIO class.

DESCRIPTION

       This object can transform .phd files (from Phil Green's phred basecaller) to and from
       Bio::Seq::Quality objects. The phd format is described in section 10 at this url:
       http://www.phrap.org/phredphrap/phred.html

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 Jean-Marc Frigerio, Frigerio@pierroton.inra.fr

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   : $swq = $stream->next_seq()
        Function: returns the next phred sequence in the stream
        Returns : Bio::Seq::Quality object
        Args    : NONE

   write_header
        Title   : write_header()
        Usage   : $seqio->write_header()
        Function: Write out the header (BEGIN_COMMENTS .. END_COMMENT) part of a phd file
        Returns : nothing
        Args    : a Bio::Seq::Quality object
        Notes   : These are the comments that reside in the header of a phd file
                  at the present time. If not provided by the Bio::Seq::Quality object,
                  the following default values will be used:

            CHROMAT_FILE          : $swq->id()
            ABI_THUMBPRINT        : 0
            PHRED_VERSION         : 0.980904.e
            CALL_METHOD           : phred
            QUALITY_LEVELS        : 99
            TIME                  : <current time>
            TRACE_ARRAY_MIN_INDEX : 0
            TRACE_ARRAY_MAX_INDEX : unknown
            CHEM                  : unknown
            DYE                   : unknown

   write_seq
        Title   : write_seq()
        Usage   : $seqio->write_seq($swq);
        Function: Write out a phd file.
        Returns : Nothing.
        Args    : a Bio::Seq::Quality object

   attribute
        Title   : attribute()
        Usage   : swq->attribute(name[,value]);
        Function: Get/Set the name attribute.
        Returns : a string if 1 param, nothing else.
        Args    : a name or a pair name, value

   chromat_file
        Title   : chromat_file
        Usage   : swq->chromat_file([filename]);
        Function: Get/Set the CHROMAT_FILE attribute.
        Returns : a string if 1 param, nothing else.
        Args    : none or a filename

   abi_thumbprint
        Title   : abi_thumbprint
        Usage   : swq->abi_thumbprint([value]);
        Function: Get/Set the ABI_THUMBPRINT attribute.
        Returns : a string if 1 param, nothing else.
        Args    : none or a value

   phred_version
        Title   : phred_version
        Usage   : swq->phred_version([value]);
        Function: Get/Set the PHRED_VERSION attribute.
        Returns : a string if 1 param, nothing else.
        Args    : none or a value

   call_method
        Title   : call_method
        Usage   : swq->call_method([value]);
        Function: Get/Set the CALL_METHOD attribute.
        Returns : a string if 1 param, nothing else.
        Args    : none or a value

   quality_levels
        Title   : quality_levels
        Usage   : swq->quality_levels([value]);
        Function: Get/Set the quality_levels attribute.
        Returns : a string if 1 param, nothing else.
        Args    : none or a value

   trace_array_min_index
        Title   : trace_array_min_index
        Usage   : swq->trace_array_min_index([value]);
        Function: Get/Set the trace_array_min_index attribute.
        Returns : a string if 1 param, nothing else.
        Args    : none or a value

   trace_array_max_index
        Title   : trace_array_max_index
        Usage   : swq->trace_array_max_index([value]);
        Function: Get/Set the trace_array_max_index attribute.
        Returns : a string if 1 param, nothing else.
        Args    : none or a value

   chem
        Title   : chem
        Usage   : swq->chem([value]);
        Function: Get/Set the chem attribute.
        Returns : a string if 1 param, nothing else.
        Args    : none or a value

   dye
        Title   : dye
        Usage   : swq->dye([value]);
        Function: Get/Set the dye attribute.
        Returns : a string if 1 param, nothing else.
        Args    : none or a value

   time
        Title   : time
        Usage   : swq->time([value]);
        Function: Get/Set the time attribute.
        Returns : a string if 1 param, nothing else.
        Args    : none or a value

   touch
        Title   : touch
        Usage   : swq->touch();
        Function: Set the time attribute to current time.
        Returns : nothing
        Args    : none