Author: Francesco Strozzi
Copyright: 2008 Francesco Strozzi   
License: The Ruby License

This module allows the parsing of the standard output of Gmap (http://www.gene.com/share/gmap/)

Example: 

   Gmap::Core.open("output.gmap") do |gmap|
   
     gmap.each_sequence do |seq|
     
       seq.each do |result|
      
         result.query (Query sequence name)
         result.target  (Target sequence name)
         result.q_start (Start coordinate of the query sequence) 
         result.q_end (End coordinate of the query sequence)
         result.start (Start coordintate of the target sequence)
         result.end (End coordinate of the target sequence) 
         result.strand (Strand of the target sequence) 
         result.exons (# exons found) 
         result.coverage (Coverage of the query sequence) 
         result.perc_identity (Pecentage of identity from the alignment)
         result.indels (# insertion or deletions) 
         result.mismatch (# mismatch)  
         result.aa_change (Prediction of AA changes from mismatches and indels found) 
         result.aln (Raw alignment between target and query sequences)
         
         ONLY IF GENE MAPS ARE USED WITH GMAP

         result.gene_start (Start coordinate of the overlapping gene)
         result.gene_end (End coordinate of the overlapping gene)
         result.gene_id (ID of the overlapping gene)
       end
   
     end
   
   end