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revision 1.1, Sun Apr 12 15:18:42 2009 UTC revision 1.2, Mon Apr 13 14:35:06 2009 UTC
# Line 16  Line 16 
16  if (-d "$dir/HTML")                 { system "rm -r $dir/HTML" }  if (-d "$dir/HTML")                 { system "rm -r $dir/HTML" }
17  if (-d "$dir/Picked")               { system "rm -r $dir/Picked" }  if (-d "$dir/Picked")               { system "rm -r $dir/Picked" }
18  if (-d "$dir/Comparisons")          { system "rm -r $dir/Comparisons" }  if (-d "$dir/Comparisons")          { system "rm -r $dir/Comparisons" }
19  &FIG::run("make_scored_instances $dir/genomes $dir/Instances $dir/ScoredAlignments $dir/HTML");  &FIG::run("make_scored_instances $dir/genomes $dir/Instances $dir/ScoredAlignments $dir/contigs $dir/HTML");
20  &FIG::run("get_rna_features_for_calling_genes $dir/genomes $dir/Instances");  &FIG::run("get_rna_features_for_calling_genes $dir/genomes $dir/Instances");
21  &FIG::run("generate_picked $dir/Instances $dir/Picked");  &FIG::run("generate_picked $dir/Instances $dir/Picked");
22  &FIG::run("mark_picked_genes genomes $dir/ScoredAlignments $dir/Picked $dir/HTML");  &FIG::run("mark_picked_genes genomes $dir/ScoredAlignments $dir/Picked $dir/HTML");

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