Merge remote-tracking branch 'origin/geoff' into gff

Incorporate fix for cross origin genes crashing islandpath.
brinkmanlab · Jun 6, 2019 · c24711b · c24711b
2 parents c8d1fe0 + 7aa93b9
commit c24711b
Showing 1 changed file with 7 additions and 1 deletion.
diff --git a/lib/GenomeUtils.pm b/lib/GenomeUtils.pm
@@ -380,12 +380,18 @@ sub read_and_convert {
 		my $count = 0;
 
 		#Step through each protein
-		foreach my $feat (@cds) {
+		PROT: foreach my $feat (@cds) {
 			$count++;
 
 			#Get the general features
 			my $start  = $feat->start;
 			my $end    = $feat->end;
+
+			# Ignore joined spans that break the trunc() function
+			if ($start > $end) {
+			    next PROT;
+			}
+
 			my $strand = $feat->strand;
 			my $length = $feat->length;