--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfvcfintersect-test1.vcf	Wed Jun 11 17:11:12 2014 -0400
@@ -0,0 +1,24 @@
+##fileformat=VCFv4.1
+##fileDate=20140610
+##source=Dan
+##reference=file:///galaxy/data/phiX/sam_index/phiX.fa
+##filter="AF > .001"
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##FORMAT=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##FORMAT=<ID=NC,Number=.,Type=String,Description="Nucleotide and indel counts">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	groupA	groupB
+phiX174	1503	.	A	C	0	.	AC=2;AF=0.0454545454545	GT:AC:AF:NC	0:0:0:A=20,C=1,	0:2:0.0833333333333:A=22,C=2,
+phiX174	1536	.	A	C	0	.	AC=3;AF=0.0545454545455	GT:AC:AF:NC	0:3:0.111111111111:A=24,C=3,	0:0:0:A=28,C=1,
+phiX174	1541	.	T	G	0	.	AC=2;AF=0.0363636363636	GT:AC:AF:NC	0:2:0.0740740740741:T=25,G=2,	0:0:0:T=28,
+phiX174	1553	.	A	G	0	.	AC=2;AF=0.0408163265306	GT:AC:AF:NC	0:2:0.0952380952381:A=19,C=1,G=2,	0:0:0:A=28,
+phiX174	1566	.	C	G	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:0:0:C=30,T=1,	0:2:0.0571428571429:C=33,G=2,
+phiX174	1572	.	T	G	0	.	AC=2;AF=0.03125	GT:AC:AF:NC	0:2:0.0625:T=30,G=2,	0:0:0:T=32,
+phiX174	1574	.	G	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.0882352941176:C=3,G=31,	0:0:0:G=34,
+phiX174	1575	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0571428571429:A=33,C=2,	0:0:0:A=33,T=1,
+phiX174	1577	.	A	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:0:0:A=35,	0:3:0.0909090909091:A=30,C=3,
+phiX174	1581	.	T	G	0	.	AC=2;AF=0.0285714285714	GT:AC:AF:NC	0:2:0.0555555555556:C=1,T=34,G=2,	0:0:0:T=34,G=1,
+phiX174	1591	.	A	C	0	.	AC=3;AF=0.037037037037	GT:AC:AF:NC	0:3:0.0789473684211:A=35,C=3,	0:0:0:A=43,C=1,
+phiX174	1597	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:2:0.0606060606061:T=31,G=2,	0:0:0:C=1,T=45,