NAME

       Bio::AlignIO::maf - Multiple Alignment Format sequence input stream

SYNOPSIS

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

        use Bio::AlignIO;

        my $alignio = Bio::AlignIO->new(-fh => \*STDIN, -format => 'maf');

        while(my $aln = $alignio->next_aln()){
          my $match_line = $aln->match_line;

          print $aln, "\n";

          print $aln->length, "\n";
          print $aln->num_residues, "\n";
          print $aln->is_flush, "\n";
          print $aln->num_sequences, "\n";

          $aln->splice_by_seq_pos(1);

          print $aln->consensus_string(60), "\n";
          print $aln->get_seq_by_pos(1)->seq, "\n";
          print $aln->match_line(), "\n";

          print "\n";
        }

DESCRIPTION

       This class constructs Bio::SimpleAlign objects from an MAF-format multiple alignment file.

       Writing in MAF format is currently unimplemented.

       Spec of MAF format is here:
         http://genome.ucsc.edu/FAQ/FAQformat

FEEDBACK

   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

AUTHORS - Allen Day

       Email: allenday@ucla.edu

APPENDIX

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

   new
        Title   : new
        Usage   : my $alignio = Bio::AlignIO->new(-format => 'maf'
                                                 -file   => '>file',
                                                 -idlength => 10,
                                                 -idlinebreak => 1);
        Function: Initialize a new L<Bio::AlignIO::maf> reader
        Returns : L<Bio::AlignIO> object
        Args    :

   next_aln
        Title   : next_aln
        Usage   : $aln = $stream->next_aln()
        Function: returns the next alignment in the stream.
                  Throws an exception if trying to read in PHYLIP
                  sequential format.
        Returns : L<Bio::SimpleAlign> object
        Args    :