removed DB_File

TransDecoder · May 11, 2018 · 7cbedac · 7cbedac
1 parent c547088
commit 7cbedac
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/util/gff3_gene_to_gtf_format.pl b/util/gff3_gene_to_gtf_format.pl
@@ -21,7 +21,7 @@
     my $fasta_retriever = new Fasta_retriever($genome_fasta);
 
     my $inx_file = "$gff3_file.tmp.inx";
-    my $gene_obj_indexer = new Gene_obj_indexer( { "create" => $inx_file } );
+    my $gene_obj_indexer = {};
 
     my $asmbl_id_to_gene_list_href = &GFF3_utils2::index_GFF3_gene_objs($gff3_file, $gene_obj_indexer);
 
@@ -37,7 +37,7 @@
         foreach my $gene_id (@gene_ids) {
 
             ## note models of isoforms are bundled into the same gene object.
-            my $gene_obj_ref = $gene_obj_indexer->get_gene($gene_id);
+            my $gene_obj_ref = $gene_obj_indexer->{$gene_id} or confess "Error, no gene_obj for $gene_id in $gff3_file";
 
             foreach my $gene_obj ($gene_obj_ref, $gene_obj_ref->get_additional_isoforms()) {