lib/bio/PolyploidTools/ExonContainer.rb in bio-polyploid-tools-0.8.6 vs lib/bio/PolyploidTools/ExonContainer.rb in bio-polyploid-tools-0.8.7

@@ -219,9 +219,10 @@
     def remove_alignments_over_max_hits
       @snp_map.each_pair do | gene, snp_array| 
         snp_array.each do |snp|
           if snp.exon_list.size > max_hits
             total_hits = snp.exon_list.size
+            snp.hit_count = total_hits
             snp.exon_list = {} 
             snp.repetitive = true
             snp.errors << "The marker is in a repetitive region (#{total_hits} hits to reference)"
           end
         end
\ No newline at end of file