NAME

       Bio::FeatureIO::bed - read/write features from UCSC BED format

SYNOPSIS

         my $in = Bio::FeatureIO(-format => 'bed', -file => 'file.bed');
         for my $feat ($in->next_feature) {
           # do something with $feat (a Bio::SeqFeature::Annotated object)
         }

         my $out = Bio::FeatureIO(-format=>'bed');
         for my $feat ($seq->get_seqFeatures) {
           $out->write_feature($feat);
         }

DESCRIPTION

       See <http://www.genome.ucsc.edu/goldenPath/help/customTrack.html#BED>.

       Currently for read and write only the first 6 fields (chr, start, end, name, score,
       strand) are supported.

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 the Bioperl mailing list.  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 of the bugs and their
       resolution. Bug reports can be submitted via the web:

         http://bugzilla.open-bio.org/

AUTHOR - Allen Day

       Email allenday@ucla.edu

CONTRIBUTORS

       Sendu Bala, bix@sendu.me.uk

APPENDIX

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

   _initialize
        Title   : _initialize
        Function: initializes BED for reading/writing
        Args    : all optional:
                  name          description
                  ----------------------------------------------------------
                  -name         the name for the BED track, stored in header
                                name defaults to localtime()
                  -description  the description for the BED track, stored in
                                header.  defaults to localtime().
                  -use_score    whether or not the score attribute of
                                features should be used when rendering them.
                                the higher the score the darker the color.
                                defaults to 0 (false)

   use_score
        Title   : use_score
        Usage   : $obj->use_score($newval)
        Function: should score be used to adjust feature color when rendering?  set to true if so.
        Example :
        Returns : value of use_score (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   name
        Title   : name
        Usage   : $obj->name($newval)
        Function: name of BED track
        Example :
        Returns : value of name (a scalar)
        Args    : on set, new value (a scalar or undef, optional)

   description
        Title   : description
        Usage   : $obj->description($newval)
        Function: description of BED track
        Example :
        Returns : value of description (a scalar)
        Args    : on set, new value (a scalar or undef, optional)