[Bioperl-l] Bio::Tools::RepeatMasker typo?

Emmanuel Quevillon equevill at infobiogen.fr
Wed Nov 2 12:16:16 EST 2005


I just played with RepeatMasker module to parse output and create GFF3.
I noticed there is (I am not sure if it is a typo or it is wanted) 
mistyped line in
function next_result() :

          my $rf = Bio::SeqFeature::Generic->new;
          $rf->seq_id          ($query_name);
          $rf->score            ($score);
          $rf->start            ($query_start);
          $rf->end              ($query_end);
          $rf->strand           ($strand);
          $rf->source_tag       ("RepeatMasker");
          $rf->primary_tag      ($repeat_class);
          my $rf2 = Bio::SeqFeature::Generic->new;
          $rf2->seq_id         ($repeat_name);
          $rf2->score           ($score);
          $rf2->start           ($hit_start);
          $rf2->end             ($hit_end);
          $rf2->strand          ($strand);
          $rf2->source_tag      ("RepeatMasker");    
          $rf->primary_tag      ($repeat_class);    <=========== Would not be $rf2 instead?

Please let me know.




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