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revision 1.13, Wed Sep 29 18:41:49 2010 UTC revision 1.14, Wed Sep 29 23:59:32 2010 UTC
# Line 454  Line 454 
454          }          }
455      }      }
456    
457        #  Do the analysis
458        #  Begin by eliminating indels from the input sequences
459        #
460        $reps2  = &gjoseqlib::pack_sequences($reps2);
461        $seqs2  = &gjoseqlib::pack_sequences($seqs2);
462    
463      if ( $by_size )      if ( $by_size )
464      {      {
465          @$reps2 = sort { length( $b->[2] ) <=> length( $a->[2] ) } @$reps2;          @$reps2 = sort { length( $b->[2] ) <=> length( $a->[2] ) } @$reps2;
# Line 768  Line 774 
774          }          }
775      }      }
776    
777    
778        #  Do the analysis
779        #  Begin by eliminating indels from the input sequences
780        #
781        $reps2  = &gjoseqlib::pack_sequences($reps2);
782        $seqs2  = &gjoseqlib::pack_sequences($seqs2);
783    
784      if ( $by_size )      if ( $by_size )
785      {      {
786          @$reps2 = sort { length( $b->[2] ) <=> length( $a->[2] ) } @$reps2;          @$reps2 = sort { length( $b->[2] ) <=> length( $a->[2] ) } @$reps2;
# Line 982  Line 995 
995      $max_ref_sim = $max_sim if ( $max_ref_sim < $max_sim );      $max_ref_sim = $max_sim if ( $max_ref_sim < $max_sim );
996    
997      #  Do the analysis      #  Do the analysis
998        #  Begin by eliminating indels from the input sequences
999        #
1000        ($ref) = &gjoseqlib::pack_sequences($ref);
1001        $seqs  = &gjoseqlib::pack_sequences($seqs);
1002    
1003      my $ref_id  = $ref->[0];      my $ref_id  = $ref->[0];
1004      my $ref_seq = $ref->[2];      my $ref_seq = $ref->[2];

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