Added unit test to intersect for gff files.

test/intersect/gdc.gff

+chr2L	.	UTR	41	70	0	+	.	ID=mRNA:xs2:UTR:41-70;Parent=mRNA:xs2;
+chr2L	.	CDS	71	130	0	+	.	ID=mRNA:xs2:CDS:71-130;Parent=mRNA:xs2;
+chr2L	.	intron	131	170	0	+	.	ID=mRNA:xs2:intron:131-170;Parent=mRNA:xs2;
+chr2L	.	CDS	171	200	0	+	.	ID=mRNA:xs2:CDS:171-200;Parent=mRNA:xs2;
+chr2L	.	UTR	201	220	0	+	.	ID=mRNA:xs2:UTR:201-220;Parent=mRNA:xs2;
+chr2L	.	exon	41	130	0	+	.	ID=mRNA:xs2:exon:41-130;Parent=mRNA:xs2;
+chr2L	.	exon	171	220	0	+	.	ID=mRNA:xs2:exon:171-220;Parent=mRNA:xs2;
+chr2L	.	mRNA	41	220	0	+	.	ID=mRNA:xs2;Parent=g2;
+chr2L	.	CDS	161	230	0	-	.	ID=tRNA:t2:CDS:161-230;Parent=tRNA:t2;
+chr2L	.	exon	161	230	0	-	.	ID=tRNA:t2:exon:161-230;Parent=tRNA:t2;
+chr2L	.	tRNA	161	230	0	-	.	ID=tRNA:t2;Parent=t2;
+chr2L	.	gene	41	220	0	+	.	ID=g2;

test/intersect/gdc_one.bed

+chr2L	50	100

test/intersect/new_test-intersect.sh

@@ -650,7 +650,19 @@ check obs exp
 rm obs exp
 
 
-
+###########################################################
+# Test that gff files work correctly
+############################################################
+echo "    intersect.new.t55...\c"
+echo \
+"chr2L	.	UTR	50	70	0	+	.	ID=mRNA:xs2:UTR:41-70;Parent=mRNA:xs2;
+chr2L	.	CDS	71	100	0	+	.	ID=mRNA:xs2:CDS:71-130;Parent=mRNA:xs2;
+chr2L	.	exon	50	100	0	+	.	ID=mRNA:xs2:exon:41-130;Parent=mRNA:xs2;
+chr2L	.	mRNA	50	100	0	+	.	ID=mRNA:xs2;Parent=g2;
+chr2L	.	gene	50	100	0	+	.	ID=g2;" > exp
+$BT intersect -a gdc.gff -b gdc_one.bed > obs
+check obs exp
+rm obs exp