# HG changeset patch
# User devteam
# Date 1426790879 14400
# Node ID b29dbe1270b58d2ed82957becdd36ba175a0a2f8

Uploaded

diff -r 000000000000 -r b29dbe1270b5 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Thu Mar 19 14:47:59 2015 -0400
@@ -0,0 +1,28 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="8a5602bf07">vcflib</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" />
+        </stdio>
+    </xml>
+   	<xml name="citations">
+   	     <citations>
+             <citation type="bibtex">
+@misc{Garrison2015,
+  author = {Garrison, Erik},
+  year = {2015},
+  title = {vcflib},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/ekg/vcflib},
+}
+             </citation>
+   	     </citations>
+   	</xml>
+    <token name="@IS_PART_OF_VCFLIB@">is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).</token>
+</macros>
diff -r 000000000000 -r b29dbe1270b5 test-data/vcflib-test-genome-phix.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcflib-test-genome-phix.fa	Thu Mar 19 14:47:59 2015 -0400
@@ -0,0 +1,2 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
diff -r 000000000000 -r b29dbe1270b5 test-data/vcfvcfintersect-input1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfvcfintersect-input1.vcf	Thu Mar 19 14:47:59 2015 -0400
@@ -0,0 +1,121 @@
+##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	1015	.	A	C	0	.	AC=2;AF=0.0555555555556	GT:AC:AF:NC	0:0,2:0,0.2:A=8,C=2,G=1,	0:0,0:0,0:A=26,G=1,
+phiX174	1016	.	A	T	0	.	AC=2;AF=0.0555555555556	GT:AC:AF:NC	0:0:0:A=10,	0:2:0.0769230769231:A=24,T=2,
+phiX174	1038	.	A	C	0	.	AC=2;AF=0.046511627907	GT:AC:AF:NC	0:2:0.153846153846:A=11,C=2,	0:0:0:A=30,
+phiX174	1045	.	T	G	0	.	AC=2;AF=0.0425531914894	GT:AC:AF:NC	0:0:0:T=15,G=1,	0:2:0.0625:T=30,G=2,
+phiX174	1048	.	C	A	0	.	AC=2;AF=0.0434782608696	GT:AC:AF:NC	0:2:0.133333333333:A=2,C=13,	0:0:0:C=31,G=1,
+phiX174	1050	.	A	C	0	.	AC=3;AF=0.0714285714286	GT:AC:AF:NC	0:0:0:A=12,	0:3:0.1:A=27,C=3,
+phiX174	1051	.	T	G	0	.	AC=2;AF=0.0487804878049	GT:AC:AF:NC	0:2:0.166666666667:C=1,T=10,G=2,	0:0:0:T=29,G=1,
+phiX174	1054	.	T	G	0	.	AC=2;AF=0.0454545454545	GT:AC:AF:NC	0:2:0.153846153846:T=11,G=2,	0:0:0:T=31,G=1,
+phiX174	1076	.	G	C	0	.	AC=2;AF=0.0363636363636	GT:AC:AF:NC	0:2:0.105263157895:A=1,C=2,G=17,	0:0:0:G=36,
+phiX174	1080	.	G	C	0	.	AC=2;AF=0.0344827586207	GT:AC:AF:NC	0:2:0.105263157895:A=1,C=2,T=1,G=17,	0:0:0:C=1,G=39,
+phiX174	1092	.	T	G	0	.	AC=2;AF=0.0263157894737	GT:AC:AF:NC	0:2:0.0833333333333:C=1,T=22,G=2,	0:0:0:T=52,G=1,
+phiX174	1093	.	T	G	0	.	AC=2;AF=0.025974025974	GT:AC:AF:NC	0:2:0.08:T=23,G=2,	0:0:0:T=52,
+phiX174	1102	.	T	C	0	.	AC=6;AF=0.0779220779221	GT:AC:AF:NC	0:2:0.0869565217391:C=2,T=21,	0:4:0.0740740740741:C=4,T=50,
+phiX174	1107	.	T	G	0	.	AC=2;AF=0.0277777777778	GT:AC:AF:NC	0:0:0:T=22,G=1,	0:2:0.04:T=48,G=2,
+phiX174	1110	.	T	C	0	.	AC=2;AF=0.0277777777778	GT:AC:AF:NC	0:2:0.125:C=2,T=14,	0:0:0:C=1,T=56,G=1,
+phiX174	1121	.	T	G	0	.	AC=3;AF=0.041095890411	GT:AC:AF:NC	0:0:0:T=19,	0:3:0.0555555555556:T=51,G=3,
+phiX174	1124	.	T	C	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:0,2:0,0.117647058824:C=2,T=15,G=1,	0:0,0:0,0:T=48,G=1,
+phiX174	1125	.	T	G	0	.	AC=3;AF=0.0454545454545	GT:AC:AF:NC	0:3:0.176470588235:T=14,G=3,	0:0:0:T=49,G=1,
+phiX174	1131	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:2:0.0952380952381:T=19,G=2,	0:0:0:T=57,
+phiX174	1141	.	T	G	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:0:0:T=20,G=1,	0:2:0.0338983050847:T=57,G=2,
+phiX174	1145	.	G	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.0952380952381:C=2,G=19,	0:0:0:G=52,
+phiX174	1147	.	T	C	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:2:0.0952380952381:C=2,T=19,	0:0:0:T=50,
+phiX174	1149	.	T	G,C	0	.	AC=2,2;AF=0.027027027027,0.027027027027	GT:AC:AF:NC	0:2,2:0.1,0.1:C=2,T=16,G=2,	0:0,0:0,0:T=54,
+phiX174	1156	.	T	G	0	.	AC=2;AF=0.031746031746	GT:AC:AF:NC	0:0:0:C=1,T=15,	0:2:0.0416666666667:T=46,G=2,
+phiX174	1159	.	T	C,G	0	.	AC=2,2;AF=0.0298507462687,0.0298507462687	GT:AC:AF:NC	0:2,0:0.111111111111,0:C=2,T=16,	0:0,2:0,0.0408163265306:C=1,T=47,G=2,
+phiX174	1164	.	T	G	0	.	AC=4;AF=0.0666666666667	GT:AC:AF:NC	0:0:0:C=1,T=16,G=1,	0:4:0.0909090909091:T=40,G=4,
+phiX174	1168	.	T	G	0	.	AC=4;AF=0.0666666666667	GT:AC:AF:NC	0:2:0.0952380952381:C=1,T=19,G=2,	0:2:0.0512820512821:T=37,G=2,
+phiX174	1171	.	T	G	0	.	AC=2;AF=0.0327868852459	GT:AC:AF:NC	0:2:0.0869565217391:T=21,G=2,	0:0:0:T=38,G=1,
+phiX174	1174	.	C	A	0	.	AC=2;AF=0.0327868852459	GT:AC:AF:NC	0:2:0.0869565217391:A=2,C=21,	0:0:0:A=1,C=38,
+phiX174	1178	.	G	C	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:2:0.0740740740741:C=2,T=1,G=25,	0:0:0:G=38,
+phiX174	1187	.	T	G	0	.	AC=3;AF=0.04	GT:AC:AF:NC	0:3:0.0882352941176:C=1,T=31,G=3,	0:0:0:T=41,
+phiX174	1189	.	T	C	0	.	AC=3;AF=0.0379746835443	GT:AC:AF:NC	0:3:0.0857142857143:C=3,T=32,G=1,	0:0:0:T=44,
+phiX174	1200	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:3:0.0882352941176:T=31,G=3,	0:0:0:T=48,G=1,
+phiX174	1202	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:0:0:T=32,	0:3:0.06:T=47,G=3,
+phiX174	1205	.	A	C	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:2:0.0588235294118:A=32,C=2,	0:0:0:A=47,C=1,G=1,
+phiX174	1207	.	T	G	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:0:0:A=1,T=34,	0:2:0.0425531914894:T=45,G=2,
+phiX174	1214	.	G	A	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:0:0:T=1,G=34,	0:2:0.0425531914894:A=2,G=45,
+phiX174	1216	.	C	A	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:0:0:C=34,	0:2:0.0425531914894:A=2,C=45,
+phiX174	1217	.	C	A	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:2:0.0588235294118:A=2,C=32,	0:0:0:C=46,
+phiX174	1219	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:0:0:C=1,T=33,G=1,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1223	.	C	T	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:2:0.0555555555556:C=34,T=2,	0:0:0:C=44,
+phiX174	1227	.	A	C	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:2:0.0588235294118:A=32,C=2,	0:0:0:A=40,
+phiX174	1232	.	T	G	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:0:0:T=34,	0:2:0.0606060606061:C=1,T=31,G=2,
+phiX174	1236	.	G	T	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0606060606061:A=1,T=2,G=31,	0:0:0:G=35,
+phiX174	1237	.	T	G	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0571428571429:A=1,T=33,G=2,	0:0:0:T=33,G=1,
+phiX174	1240	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:0,0:0,0:A=32,T=1,	0:0,2:0,0.0555555555556:A=34,C=2,T=1,
+phiX174	1245	.	G	T	0	.	AC=4;AF=0.0625	GT:AC:AF:NC	0:2:0.0666666666667:C=1,T=2,G=28,	0:2:0.0588235294118:T=2,G=32,
+phiX174	1247	.	A	T	0	.	AC=2;AF=0.031746031746	GT:AC:AF:NC	0:2:0.0714285714286:A=26,C=1,T=2,G=1,	0:0:0:A=35,
+phiX174	1250	.	A	C	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:2:0.0769230769231:A=24,C=2,	0:0:0:A=39,
+phiX174	1251	.	A	G	0	.	AC=3;AF=0.044776119403	GT:AC:AF:NC	0:0:0:A=29,	0:3:0.0789473684211:A=35,C=1,G=3,
+phiX174	1253	.	T	G	0	.	AC=4;AF=0.0526315789474	GT:AC:AF:NC	0:2:0.0645161290323:T=29,G=2,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1257	.	T	G	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:0:0:T=26,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1259	.	A	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:0:0:A=28,T=1,	0:2:0.0444444444444:A=43,C=2,G=1,
+phiX174	1274	.	G	C	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.0512820512821:C=2,G=37,	0:0:0:G=44,
+phiX174	1277	.	A	C	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:2:0.05:A=38,C=2,	0:0:0:A=40,G=1,
+phiX174	1279	.	T	G	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:0:0:T=39,G=1,	0:2:0.05:C=1,T=38,G=2,
+phiX174	1284	.	T	G,C	0	.	AC=3,2;AF=0.038961038961,0.025974025974	GT:AC:AF:NC	0:3,2:0.075,0.05:C=2,T=35,G=3,	0:0,0:0,0:A=1,T=37,
+phiX174	1289	.	A	C	0	.	AC=3;AF=0.0454545454545	GT:AC:AF:NC	0:3:0.0789473684211:A=35,C=3,	0:0:0:A=28,G=1,
+phiX174	1296	.	A	C	0	.	AC=2;AF=0.03125	GT:AC:AF:NC	0:0:0:A=38,	0:2:0.0769230769231:A=24,C=2,
+phiX174	1298	.	A	C	0	.	AC=3;AF=0.0491803278689	GT:AC:AF:NC	0:3,0:0.0810810810811,0:A=34,C=3,G=1,	0:0,0:0,0:A=24,C=1,T=1,G=1,
+phiX174	1306	.	T	G	0	.	AC=5;AF=0.0943396226415	GT:AC:AF:NC	0:5:0.178571428571:T=23,G=5,	0:0:0:C=1,T=25,
+phiX174	1307	.	T	G	0	.	AC=3;AF=0.0545454545455	GT:AC:AF:NC	0:3:0.107142857143:T=25,G=3,	0:0:0:C=1,T=27,
+phiX174	1314	.	A	G	0	.	AC=5;AF=0.0877192982456	GT:AC:AF:NC	0:2,0:0.0740740740741,0:A=25,C=1,G=2,	0:3,0:0.1,0:A=27,C=1,G=3,
+phiX174	1317	.	A	C	0	.	AC=2;AF=0.0322580645161	GT:AC:AF:NC	0:2:0.0740740740741:A=25,C=2,	0:0:0:A=35,
+phiX174	1320	.	C	G	0	.	AC=2;AF=0.0322580645161	GT:AC:AF:NC	0:2:0.0769230769231:C=24,G=2,	0:0:0:C=36,
+phiX174	1322	.	G	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.107142857143:C=3,G=25,	0:0:0:G=40,
+phiX174	1323	.	C	G	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:0:0:C=28,	0:2:0.0512820512821:C=37,T=1,G=2,
+phiX174	1329	.	T	C	0	.	AC=2;AF=0.0277777777778	GT:AC:AF:NC	0:2:0.0666666666667:C=2,T=28,	0:0:0:T=42,G=1,
+phiX174	1335	.	C	A	0	.	AC=2;AF=0.025974025974	GT:AC:AF:NC	0:2:0.0625:A=2,C=30,	0:0:0:C=45,
+phiX174	1338	.	T	A	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:0:0:T=32,	0:2:0.047619047619:A=2,T=40,
+phiX174	1345	.	T	C	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:0,0:0,0:T=36,G=1,	0:0,2:0,0.046511627907:C=2,T=41,G=1,
+phiX174	1347	.	A	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0512820512821:A=37,C=2,G=1,	0:0:0:A=43,
+phiX174	1348	.	T	G	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.05:T=38,G=2,	0:0:0:T=43,
+phiX174	1352	.	A	T	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:0:0:A=34,G=1,	0:2:0.0512820512821:A=37,T=2,
+phiX174	1354	.	T	G,A	0	.	AC=2,2;AF=0.027027027027,0.027027027027	GT:AC:AF:NC	0:2,0:0.0526315789474,0:T=36,G=2,	0:0,2:0,0.0555555555556:A=2,T=34,G=1,
+phiX174	1359	.	T	G	0	.	AC=3;AF=0.0405405405405	GT:AC:AF:NC	0:3:0.0714285714286:T=39,G=3,	0:0:0:T=32,G=1,
+phiX174	1366	.	G	C	0	.	AC=3;AF=0.0428571428571	GT:AC:AF:NC	0:3:0.0714285714286:C=3,T=1,G=39,	0:0:0:G=28,
+phiX174	1370	.	T	G	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:0:0:C=1,T=45,G=1,	0:2:0.0833333333333:A=1,T=22,G=2,
+phiX174	1373	.	T	G	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:2:0.0408163265306:T=47,G=2,	0:0:0:T=25,
+phiX174	1380	.	G	C	0	.	AC=2;AF=0.0238095238095	GT:AC:AF:NC	0:0,2:0,0.0384615384615:C=2,T=1,G=50,	0:0,0:0,0:T=1,G=32,
+phiX174	1381	.	T	G	0	.	AC=3;AF=0.0361445783133	GT:AC:AF:NC	0:3:0.0576923076923:A=1,T=49,G=3,	0:0:0:T=31,
+phiX174	1384	.	T	G	0	.	AC=4;AF=0.0512820512821	GT:AC:AF:NC	0:4:0.0816326530612:T=45,G=4,	0:0:0:T=29,G=1,
+phiX174	1385	.	T	G	0	.	AC=4;AF=0.0512820512821	GT:AC:AF:NC	0:4:0.0816326530612:T=45,G=4,	0:0:0:C=1,T=29,
+phiX174	1391	.	A	C	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:2:0.0408163265306:A=47,C=2,	0:0:0:A=30,C=1,
+phiX174	1393	.	C	A	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:2:0.0425531914894:A=2,C=45,	0:0:0:C=32,
+phiX174	1396	.	T	G	0	.	AC=3;AF=0.04	GT:AC:AF:NC	0:3:0.0697674418605:T=40,G=3,	0:0:0:T=32,
+phiX174	1397	.	A	C	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:0:0:A=42,T=1,	0:2:0.0625:A=30,C=2,
+phiX174	1400	.	A	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.047619047619:A=40,C=2,G=1,	0:0:0:A=31,
+phiX174	1401	.	A	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.047619047619:A=40,C=2,	0:0:0:A=31,
+phiX174	1434	.	C	T	0	.	AC=2;AF=0.0571428571429	GT:AC:AF:NC	0:2:0.142857142857:C=12,T=2,	0:0:0:C=21,
+phiX174	1438	.	G	C	0	.	AC=2;AF=0.0526315789474	GT:AC:AF:NC	0:0:0:G=15,	0:2:0.0869565217391:C=2,G=21,
+phiX174	1450	.	T	G	0	.	AC=3;AF=0.0789473684211	GT:AC:AF:NC	0:3:0.176470588235:A=1,C=1,T=14,G=3,	0:0:0:T=21,G=1,
+phiX174	1459	.	T	G	0	.	AC=3;AF=0.075	GT:AC:AF:NC	0:3:0.142857142857:C=1,T=18,G=3,	0:0:0:T=19,
+phiX174	1470	.	C	A	0	.	AC=2;AF=0.0384615384615	GT:AC:AF:NC	0:0:0:C=29,	0:2:0.0869565217391:A=2,C=21,
+phiX174	1484	.	C	G	0	.	AC=2;AF=0.0384615384615	GT:AC:AF:NC	0:2:0.0740740740741:A=1,C=25,G=2,	0:0:0:C=25,
+phiX174	1487	.	T	G	0	.	AC=2;AF=0.0363636363636	GT:AC:AF:NC	0:2:0.0689655172414:T=27,G=2,	0:0:0:T=26,
+phiX174	1491	.	G	T	0	.	AC=2;AF=0.037037037037	GT:AC:AF:NC	0:0:0:T=1,G=26,	0:2:0.0714285714286:T=2,G=26,
+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,
diff -r 000000000000 -r b29dbe1270b5 test-data/vcfvcfintersect-input2.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfvcfintersect-input2.vcf	Thu Mar 19 14:47:59 2015 -0400
@@ -0,0 +1,122 @@
+##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,
+phiX174	1603	.	T	G	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0625:T=30,G=2,	0:0:0:T=50,
+phiX174	1606	.	T	G	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0666666666667:A=1,C=1,T=28,G=2,	0:0:0:T=52,
+phiX174	1611	.	A	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0769230769231:A=24,C=2,	0:0:0:A=56,C=1,
+phiX174	1613	.	A	G	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:0:0:A=25,C=1,G=1,	0:2:0.0344827586207:A=56,G=2,
+phiX174	1618	.	C	A	0	.	AC=2;AF=0.0229885057471	GT:AC:AF:NC	0:2:0.0666666666667:A=2,C=28,G=1,	0:0:0:A=1,C=57,
+phiX174	1619	.	C	A	0	.	AC=2;AF=0.0229885057471	GT:AC:AF:NC	0:2:0.0666666666667:A=2,C=28,	0:0:0:C=57,
+phiX174	1621	.	A	C	0	.	AC=3;AF=0.0352941176471	GT:AC:AF:NC	0:0:0:A=31,T=1,G=1,	0:3:0.0555555555556:A=51,C=3,
+phiX174	1622	.	G	T	0	.	AC=2;AF=0.0224719101124	GT:AC:AF:NC	0:0:0:A=1,G=35,	0:2:0.037037037037:T=2,G=52,
+phiX174	1624	.	A	G	0	.	AC=2;AF=0.0235294117647	GT:AC:AF:NC	0:2:0.0555555555556:A=34,T=1,G=2,	0:0:0:A=49,
+phiX174	1627	.	T	G,C	0	.	AC=2,2;AF=0.0246913580247,0.0246913580247	GT:AC:AF:NC	0:0,0:0,0:T=37,G=1,	0:2,2:0.0454545454545,0.0454545454545:C=2,T=40,G=2,
+phiX174	1630	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:2:0.0526315789474:C=1,T=36,G=2,	0:0:0:T=40,
+phiX174	1632	.	A	C	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:2:0.05:A=38,C=2,	0:0:0:A=41,
+phiX174	1634	.	T	G	0	.	AC=4;AF=0.0493827160494	GT:AC:AF:NC	0:2:0.047619047619:C=1,T=40,G=2,	0:2:0.0512820512821:T=37,G=2,
+phiX174	1635	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:3:0.0714285714286:T=39,G=3,	0:0:0:T=40,
+phiX174	1639	.	G	A	0	.	AC=3;AF=0.0405405405405	GT:AC:AF:NC	0:3:0.075:A=3,T=1,G=37,	0:0:0:G=34,
+phiX174	1645	.	T	G	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:2:0.0425531914894:T=45,G=2,	0:0:0:T=27,G=1,
+phiX174	1647	.	A	T,G,C	0	.	AC=2,2,2;AF=0.0253164556962,0.0253164556962,0.0253164556962	GT:AC:AF:NC	0:0,2,2:0,0.0384615384615,0.0384615384615:A=48,C=2,G=2,	0:2,0,0:0.0740740740741,0,0:A=25,T=2,
+phiX174	1652	.	G	A	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.037037037037:A=2,G=52,	0:0:0:G=29,
+phiX174	1656	.	T	G	0	.	AC=3;AF=0.0348837209302	GT:AC:AF:NC	0:3:0.0555555555556:T=51,G=3,	0:0:0:T=32,G=1,
+phiX174	1658	.	A	C	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.04:A=48,C=2,	0:0:0:A=33,
+phiX174	1659	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:3:0.0625:C=1,T=45,G=3,	0:0:0:T=34,
+phiX174	1663	.	T	G	0	.	AC=4;AF=0.0454545454545	GT:AC:AF:NC	0:0:0:A=1,T=53,	0:4:0.114285714286:T=31,G=4,
+phiX174	1665	.	C	A	0	.	AC=2;AF=0.0212765957447	GT:AC:AF:NC	0:2:0.0384615384615:A=2,C=50,G=1,	0:0:0:C=42,
+phiX174	1670	.	G	C	0	.	AC=2;AF=0.0224719101124	GT:AC:AF:NC	0:0,2:0,0.0408163265306:A=1,C=2,T=1,G=47,	0:0,0:0,0:T=1,G=40,
+phiX174	1671	.	G	T	0	.	AC=2;AF=0.0212765957447	GT:AC:AF:NC	0:2:0.0384615384615:C=1,T=2,G=50,	0:0:0:G=42,
+phiX174	1672	.	A	G	0	.	AC=3;AF=0.0315789473684	GT:AC:AF:NC	0:3:0.0545454545455:A=52,G=3,	0:0:0:A=40,T=1,
+phiX174	1673	.	G	T	0	.	AC=2;AF=0.0212765957447	GT:AC:AF:NC	0:2:0.0377358490566:C=1,T=2,G=51,	0:0:0:G=41,
+phiX174	1674	.	G	T	0	.	AC=4;AF=0.04	GT:AC:AF:NC	0:4:0.0714285714286:T=4,G=52,	0:0:0:G=44,
+phiX174	1677	.	A	C	0	.	AC=3;AF=0.031914893617	GT:AC:AF:NC	0:3:0.0566037735849:A=50,C=3,N=1,	0:0:0:A=41,
+phiX174	1678	.	A	C	0	.	AC=2;AF=0.0212765957447	GT:AC:AF:NC	0:0:0:A=54,C=1,G=1,	0:2:0.05:A=38,C=2,
+phiX174	1682	.	T	C	0	.	AC=2;AF=0.0229885057471	GT:AC:AF:NC	0:2:0.0408163265306:C=2,T=47,G=1,	0:0:0:C=1,T=38,
+phiX174	1685	.	T	G	0	.	AC=2;AF=0.0238095238095	GT:AC:AF:NC	0:2:0.046511627907:A=1,T=41,G=2,	0:0:0:T=41,G=1,
+phiX174	1686	.	A	C	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:0:0:A=39,C=1,T=1,G=1,	0:2:0.0512820512821:A=37,C=2,
+phiX174	1687	.	T	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.047619047619:C=2,T=40,	0:0:0:A=1,T=40,
+phiX174	1688	.	G	C	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:2:0.05:C=2,T=1,G=38,	0:0:0:G=41,
+phiX174	1689	.	A	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0487804878049:A=39,C=2,T=1,G=1,	0:0:0:A=41,C=1,
+phiX174	1691	.	G	C	0	.	AC=2;AF=0.025974025974	GT:AC:AF:NC	0:2:0.05:C=2,T=1,G=38,	0:0:0:G=37,
+phiX174	1693	.	T	G	0	.	AC=2;AF=0.0238095238095	GT:AC:AF:NC	0:0:0:T=42,G=1,	0:2:0.047619047619:T=40,G=2,
+phiX174	1695	.	A	C	0	.	AC=2;AF=0.0232558139535	GT:AC:AF:NC	0:2:0.046511627907:A=41,C=2,	0:0:0:A=43,C=1,
+phiX174	1702	.	T	C	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:2:0.0512820512821:A=1,C=2,T=37,	0:0:0:C=1,T=42,
+phiX174	1707	.	T	C	0	.	AC=2;AF=0.0232558139535	GT:AC:AF:NC	0:2:0.05:C=2,T=38,	0:0:0:T=46,G=1,
+phiX174	1708	.	A	C	0	.	AC=2;AF=0.0238095238095	GT:AC:AF:NC	0:2:0.0526315789474:A=36,C=2,	0:0:0:A=46,C=1,G=1,
+phiX174	1710	.	T	C	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:0:0:C=1,T=34,	0:2:0.0434782608696:C=2,T=44,
+phiX174	1723	.	T	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0588235294118:C=2,T=32,	0:0:0:T=48,
+phiX174	1724	.	A	C	0	.	AC=4;AF=0.0481927710843	GT:AC:AF:NC	0:2:0.0571428571429:A=33,C=2,	0:2:0.0416666666667:A=46,C=2,
+phiX174	1725	.	A	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0606060606061:A=31,C=2,	0:0:0:A=49,
+phiX174	1726	.	T	G	0	.	AC=3;AF=0.037037037037	GT:AC:AF:NC	0:3:0.0882352941176:T=31,G=3,	0:0:0:C=1,T=47,
+phiX174	1730	.	T	G	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:0:0:C=1,T=28,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1739	.	G	T	0	.	AC=3;AF=0.0434782608696	GT:AC:AF:NC	0:3:0.09375:T=3,G=29,	0:0:0:G=37,
+phiX174	1746	.	A	C	0	.	AC=2;AF=0.0338983050847	GT:AC:AF:NC	0:2:0.0689655172414:A=27,C=2,	0:0:0:A=30,C=1,G=1,
+phiX174	1749	.	T	G,C	0	.	AC=3,2;AF=0.044776119403,0.0298507462687	GT:AC:AF:NC	0:3,2:0.0857142857143,0.0571428571429:C=2,T=30,G=3,	0:0,0:0,0:T=32,G=1,
+phiX174	1755	.	G	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.05:C=2,G=38,	0:0:0:C=1,G=33,
+phiX174	1756	.	A	G,C	0	.	AC=2,2;AF=0.0281690140845,0.0281690140845	GT:AC:AF:NC	0:0,2:0,0.0526315789474:A=36,C=2,T=1,G=1,	0:2,0:0.0606060606061,0:A=31,C=1,G=2,
+phiX174	1761	.	A	G	0	.	AC=2;AF=0.0285714285714	GT:AC:AF:NC	0:2:0.0512820512821:A=37,C=1,G=2,	0:0:0:A=31,
+phiX174	1764	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.05:A=38,C=2,	0:0:0:A=28,
+phiX174	1766	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0487804878049:A=39,C=2,	0:0:0:A=27,
+phiX174	1769	.	T	G	0	.	AC=2;AF=0.03125	GT:AC:AF:NC	0:2:0.0526315789474:A=1,C=1,T=36,G=2,	0:0:0:T=26,G=1,
+phiX174	1771	.	G	C	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:2:0.0526315789474:C=2,G=36,	0:0:0:G=29,
+phiX174	1772	.	T	G	0	.	AC=4;AF=0.0597014925373	GT:AC:AF:NC	0:4:0.108108108108:C=1,T=33,G=4,	0:0:0:T=30,
+phiX174	1774	.	A	G	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.0810810810811:A=34,G=3,	0:0:0:A=31,
+phiX174	1775	.	G	A	0	.	AC=2;AF=0.030303030303	GT:AC:AF:NC	0:2:0.0571428571429:A=2,G=33,	0:0:0:G=31,
+phiX174	1776	.	G	T	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:2:0.0540540540541:T=2,G=35,	0:0:0:G=32,
+phiX174	1778	.	C	G	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:2:0.0526315789474:C=36,G=2,	0:0:0:C=31,
+phiX174	1779	.	A	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.075:A=37,C=3,	0:0:0:A=28,
+phiX174	1781	.	T	G	0	.	AC=5;AF=0.0714285714286	GT:AC:AF:NC	0:2:0.0487804878049:C=1,T=39,G=2,	0:3:0.103448275862:T=26,G=3,
+phiX174	1782	.	T	G	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.075:T=37,G=3,	0:0:0:A=1,T=28,
+phiX174	1783	.	T	C	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:2:0.0512820512821:C=2,T=37,	0:0:0:T=28,G=1,
+phiX174	1788	.	G	T	0	.	AC=2;AF=0.0344827586207	GT:AC:AF:NC	0:0:0:A=1,T=1,G=29,	0:2:0.0689655172414:T=2,G=27,
+phiX174	1792	.	T	G	0	.	AC=2;AF=0.0344827586207	GT:AC:AF:NC	0:2:0.0606060606061:T=31,G=2,	0:0:0:T=25,G=1,
+phiX174	1802	.	A	C	0	.	AC=2;AF=0.030303030303	GT:AC:AF:NC	0:2:0.0571428571429:A=33,C=2,	0:0:0:A=31,C=1,
+phiX174	1804	.	C	T	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0588235294118:A=1,C=32,T=2,	0:0:0:C=34,
+phiX174	1805	.	T	G	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.0857142857143:T=32,G=3,	0:0:0:T=33,G=1,
+phiX174	1806	.	A	C	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:2:0.0571428571429:A=33,C=2,	0:0:0:A=34,G=1,
+phiX174	1824	.	G	C	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:2:0.0714285714286:C=2,T=1,G=26,	0:0:0:G=43,
+phiX174	1825	.	T	G	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:2:0.0689655172414:T=27,G=2,	0:0:0:T=42,G=1,
+phiX174	1833	.	T	G	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:0:0:A=1,T=24,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1843	.	T	G	0	.	AC=2;AF=0.031746031746	GT:AC:AF:NC	0:2:0.08:A=1,T=23,G=2,	0:0:0:T=38,
+phiX174	1847	.	A	C	0	.	AC=2;AF=0.0333333333333	GT:AC:AF:NC	0:2:0.0833333333333:A=22,C=2,T=1,G=1,	0:0:0:A=36,
+phiX174	1854	.	T	G	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:0:0:T=26,	0:2:0.0487804878049:T=39,G=2,
+phiX174	1860	.	T	G	0	.	AC=2;AF=0.0377358490566	GT:AC:AF:NC	0:0:0:A=1,T=20,	0:2:0.0606060606061:T=31,G=2,
+phiX174	1863	.	C	G	0	.	AC=2;AF=0.0384615384615	GT:AC:AF:NC	0:2:0.105263157895:A=1,C=17,G=2,	0:0:0:C=33,
+phiX174	1866	.	T	G	0	.	AC=2;AF=0.04	GT:AC:AF:NC	0:0:0:T=19,G=1,	0:2:0.0645161290323:T=29,G=2,
+phiX174	1875	.	T	A	0	.	AC=2;AF=0.0377358490566	GT:AC:AF:NC	0:2:0.0952380952381:A=2,T=19,	0:0:0:T=32,G=1,
+phiX174	1876	.	T	G	0	.	AC=3;AF=0.0588235294118	GT:AC:AF:NC	0:3:0.157894736842:C=1,T=16,G=3,	0:0:0:T=32,G=1,
+phiX174	1882	.	T	G	0	.	AC=2;AF=0.0377358490566	GT:AC:AF:NC	0:2:0.105263157895:T=17,G=2,	0:0:0:T=34,
+phiX174	1889	.	A	C	0	.	AC=2;AF=0.04	GT:AC:AF:NC	0:2:0.0869565217391:A=21,C=2,	0:0:0:A=27,
+phiX174	1913	.	G	C	0	.	AC=2;AF=0.04	GT:AC:AF:NC	0:0:0:G=27,	0:2:0.0869565217391:C=2,G=21,
+phiX174	1915	.	T	G	0	.	AC=2;AF=0.0425531914894	GT:AC:AF:NC	0:0:0:A=1,T=24,	0:2:0.0869565217391:T=21,G=2,
+phiX174	1917	.	A	T	0	.	AC=2;AF=0.0444444444444	GT:AC:AF:NC	0:2,0:0.0833333333333,0:A=22,T=2,G=1,	0:0,0:0,0:A=21,G=1,
+phiX174	1930	.	T	A	0	.	AC=2;AF=0.0526315789474	GT:AC:AF:NC	0:2:0.0909090909091:A=2,T=20,	0:0:0:T=16,
+phiX174	1934	.	A	C	0	.	AC=2;AF=0.0512820512821	GT:AC:AF:NC	0:2:0.0952380952381:A=19,C=2,T=1,	0:0:0:A=18,C=1,
+phiX174	1940	.	A	C	0	.	AC=2;AF=0.046511627907	GT:AC:AF:NC	0:2:0.0952380952381:A=19,C=2,	0:0:0:A=22,C=1,
+phiX174	1942	.	T	G	0	.	AC=2;AF=0.047619047619	GT:AC:AF:NC	0:0:0:T=19,	0:2:0.0869565217391:T=21,G=2,
+phiX174	1945	.	T	G	0	.	AC=3;AF=0.0769230769231	GT:AC:AF:NC	0:0:0:T=15,G=1,	0:3:0.125:T=21,G=3,
+phiX174	1954	.	T	C	0	.	AC=2;AF=0.0625	GT:AC:AF:NC	0:0,0:0,0:T=12,G=1,	0:0,2:0,0.1:C=2,T=18,G=1,
+phiX174	1959	.	T	G	0	.	AC=2;AF=0.0555555555556	GT:AC:AF:NC	0:2:0.153846153846:T=11,G=2,	0:0:0:T=23,
+phiX174	1994	.	A	C	0	.	AC=2;AF=0.0512820512821	GT:AC:AF:NC	0:2:0.153846153846:A=11,C=2,	0:0:0:A=26,
+phiX174	1998	.	A	G	0	.	AC=2;AF=0.05	GT:AC:AF:NC	0:2:0.142857142857:A=12,G=2,	0:0:0:A=26,
diff -r 000000000000 -r b29dbe1270b5 test-data/vcfvcfintersect-test1.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfvcfintersect-test1.vcf	Thu Mar 19 14:47:59 2015 -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,
diff -r 000000000000 -r b29dbe1270b5 test-data/vcfvcfintersect-test2.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcfvcfintersect-test2.vcf	Thu Mar 19 14:47:59 2015 -0400
@@ -0,0 +1,219 @@
+##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	1015	.	A	C	0	.	AC=2;AF=0.0555555555556	GT:AC:AF:NC	0:0,2:0,0.2:A=8,C=2,G=1,	0:0,0:0,0:A=26,G=1,
+phiX174	1016	.	A	T	0	.	AC=2;AF=0.0555555555556	GT:AC:AF:NC	0:0:0:A=10,	0:2:0.0769230769231:A=24,T=2,
+phiX174	1038	.	A	C	0	.	AC=2;AF=0.046511627907	GT:AC:AF:NC	0:2:0.153846153846:A=11,C=2,	0:0:0:A=30,
+phiX174	1045	.	T	G	0	.	AC=2;AF=0.0425531914894	GT:AC:AF:NC	0:0:0:T=15,G=1,	0:2:0.0625:T=30,G=2,
+phiX174	1048	.	C	A	0	.	AC=2;AF=0.0434782608696	GT:AC:AF:NC	0:2:0.133333333333:A=2,C=13,	0:0:0:C=31,G=1,
+phiX174	1050	.	A	C	0	.	AC=3;AF=0.0714285714286	GT:AC:AF:NC	0:0:0:A=12,	0:3:0.1:A=27,C=3,
+phiX174	1051	.	T	G	0	.	AC=2;AF=0.0487804878049	GT:AC:AF:NC	0:2:0.166666666667:C=1,T=10,G=2,	0:0:0:T=29,G=1,
+phiX174	1054	.	T	G	0	.	AC=2;AF=0.0454545454545	GT:AC:AF:NC	0:2:0.153846153846:T=11,G=2,	0:0:0:T=31,G=1,
+phiX174	1076	.	G	C	0	.	AC=2;AF=0.0363636363636	GT:AC:AF:NC	0:2:0.105263157895:A=1,C=2,G=17,	0:0:0:G=36,
+phiX174	1080	.	G	C	0	.	AC=2;AF=0.0344827586207	GT:AC:AF:NC	0:2:0.105263157895:A=1,C=2,T=1,G=17,	0:0:0:C=1,G=39,
+phiX174	1092	.	T	G	0	.	AC=2;AF=0.0263157894737	GT:AC:AF:NC	0:2:0.0833333333333:C=1,T=22,G=2,	0:0:0:T=52,G=1,
+phiX174	1093	.	T	G	0	.	AC=2;AF=0.025974025974	GT:AC:AF:NC	0:2:0.08:T=23,G=2,	0:0:0:T=52,
+phiX174	1102	.	T	C	0	.	AC=6;AF=0.0779220779221	GT:AC:AF:NC	0:2:0.0869565217391:C=2,T=21,	0:4:0.0740740740741:C=4,T=50,
+phiX174	1107	.	T	G	0	.	AC=2;AF=0.0277777777778	GT:AC:AF:NC	0:0:0:T=22,G=1,	0:2:0.04:T=48,G=2,
+phiX174	1110	.	T	C	0	.	AC=2;AF=0.0277777777778	GT:AC:AF:NC	0:2:0.125:C=2,T=14,	0:0:0:C=1,T=56,G=1,
+phiX174	1121	.	T	G	0	.	AC=3;AF=0.041095890411	GT:AC:AF:NC	0:0:0:T=19,	0:3:0.0555555555556:T=51,G=3,
+phiX174	1124	.	T	C	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:0,2:0,0.117647058824:C=2,T=15,G=1,	0:0,0:0,0:T=48,G=1,
+phiX174	1125	.	T	G	0	.	AC=3;AF=0.0454545454545	GT:AC:AF:NC	0:3:0.176470588235:T=14,G=3,	0:0:0:T=49,G=1,
+phiX174	1131	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:2:0.0952380952381:T=19,G=2,	0:0:0:T=57,
+phiX174	1141	.	T	G	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:0:0:T=20,G=1,	0:2:0.0338983050847:T=57,G=2,
+phiX174	1145	.	G	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.0952380952381:C=2,G=19,	0:0:0:G=52,
+phiX174	1147	.	T	C	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:2:0.0952380952381:C=2,T=19,	0:0:0:T=50,
+phiX174	1149	.	T	G,C	0	.	AC=2,2;AF=0.027027027027,0.027027027027	GT:AC:AF:NC	0:2,2:0.1,0.1:C=2,T=16,G=2,	0:0,0:0,0:T=54,
+phiX174	1156	.	T	G	0	.	AC=2;AF=0.031746031746	GT:AC:AF:NC	0:0:0:C=1,T=15,	0:2:0.0416666666667:T=46,G=2,
+phiX174	1159	.	T	C,G	0	.	AC=2,2;AF=0.0298507462687,0.0298507462687	GT:AC:AF:NC	0:2,0:0.111111111111,0:C=2,T=16,	0:0,2:0,0.0408163265306:C=1,T=47,G=2,
+phiX174	1164	.	T	G	0	.	AC=4;AF=0.0666666666667	GT:AC:AF:NC	0:0:0:C=1,T=16,G=1,	0:4:0.0909090909091:T=40,G=4,
+phiX174	1168	.	T	G	0	.	AC=4;AF=0.0666666666667	GT:AC:AF:NC	0:2:0.0952380952381:C=1,T=19,G=2,	0:2:0.0512820512821:T=37,G=2,
+phiX174	1171	.	T	G	0	.	AC=2;AF=0.0327868852459	GT:AC:AF:NC	0:2:0.0869565217391:T=21,G=2,	0:0:0:T=38,G=1,
+phiX174	1174	.	C	A	0	.	AC=2;AF=0.0327868852459	GT:AC:AF:NC	0:2:0.0869565217391:A=2,C=21,	0:0:0:A=1,C=38,
+phiX174	1178	.	G	C	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:2:0.0740740740741:C=2,T=1,G=25,	0:0:0:G=38,
+phiX174	1187	.	T	G	0	.	AC=3;AF=0.04	GT:AC:AF:NC	0:3:0.0882352941176:C=1,T=31,G=3,	0:0:0:T=41,
+phiX174	1189	.	T	C	0	.	AC=3;AF=0.0379746835443	GT:AC:AF:NC	0:3:0.0857142857143:C=3,T=32,G=1,	0:0:0:T=44,
+phiX174	1200	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:3:0.0882352941176:T=31,G=3,	0:0:0:T=48,G=1,
+phiX174	1202	.	T	G	0	.	AC=3;AF=0.0365853658537	GT:AC:AF:NC	0:0:0:T=32,	0:3:0.06:T=47,G=3,
+phiX174	1205	.	A	C	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:2:0.0588235294118:A=32,C=2,	0:0:0:A=47,C=1,G=1,
+phiX174	1207	.	T	G	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:0:0:A=1,T=34,	0:2:0.0425531914894:T=45,G=2,
+phiX174	1214	.	G	A	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:0:0:T=1,G=34,	0:2:0.0425531914894:A=2,G=45,
+phiX174	1216	.	C	A	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:0:0:C=34,	0:2:0.0425531914894:A=2,C=45,
+phiX174	1217	.	C	A	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:2:0.0588235294118:A=2,C=32,	0:0:0:C=46,
+phiX174	1219	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:0:0:C=1,T=33,G=1,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1223	.	C	T	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:2:0.0555555555556:C=34,T=2,	0:0:0:C=44,
+phiX174	1227	.	A	C	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:2:0.0588235294118:A=32,C=2,	0:0:0:A=40,
+phiX174	1232	.	T	G	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:0:0:T=34,	0:2:0.0606060606061:C=1,T=31,G=2,
+phiX174	1236	.	G	T	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0606060606061:A=1,T=2,G=31,	0:0:0:G=35,
+phiX174	1237	.	T	G	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:2:0.0571428571429:A=1,T=33,G=2,	0:0:0:T=33,G=1,
+phiX174	1240	.	A	C	0	.	AC=2;AF=0.0294117647059	GT:AC:AF:NC	0:0,0:0,0:A=32,T=1,	0:0,2:0,0.0555555555556:A=34,C=2,T=1,
+phiX174	1245	.	G	T	0	.	AC=4;AF=0.0625	GT:AC:AF:NC	0:2:0.0666666666667:C=1,T=2,G=28,	0:2:0.0588235294118:T=2,G=32,
+phiX174	1247	.	A	T	0	.	AC=2;AF=0.031746031746	GT:AC:AF:NC	0:2:0.0714285714286:A=26,C=1,T=2,G=1,	0:0:0:A=35,
+phiX174	1250	.	A	C	0	.	AC=2;AF=0.0307692307692	GT:AC:AF:NC	0:2:0.0769230769231:A=24,C=2,	0:0:0:A=39,
+phiX174	1251	.	A	G	0	.	AC=3;AF=0.044776119403	GT:AC:AF:NC	0:0:0:A=29,	0:3:0.0789473684211:A=35,C=1,G=3,
+phiX174	1253	.	T	G	0	.	AC=4;AF=0.0526315789474	GT:AC:AF:NC	0:2:0.0645161290323:T=29,G=2,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1257	.	T	G	0	.	AC=2;AF=0.0281690140845	GT:AC:AF:NC	0:0:0:T=26,	0:2:0.0444444444444:T=43,G=2,
+phiX174	1259	.	A	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:0:0:A=28,T=1,	0:2:0.0444444444444:A=43,C=2,G=1,
+phiX174	1274	.	G	C	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.0512820512821:C=2,G=37,	0:0:0:G=44,
+phiX174	1277	.	A	C	0	.	AC=2;AF=0.025	GT:AC:AF:NC	0:2:0.05:A=38,C=2,	0:0:0:A=40,G=1,
+phiX174	1279	.	T	G	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:0:0:T=39,G=1,	0:2:0.05:C=1,T=38,G=2,
+phiX174	1284	.	T	G,C	0	.	AC=3,2;AF=0.038961038961,0.025974025974	GT:AC:AF:NC	0:3,2:0.075,0.05:C=2,T=35,G=3,	0:0,0:0,0:A=1,T=37,
+phiX174	1289	.	A	C	0	.	AC=3;AF=0.0454545454545	GT:AC:AF:NC	0:3:0.0789473684211:A=35,C=3,	0:0:0:A=28,G=1,
+phiX174	1296	.	A	C	0	.	AC=2;AF=0.03125	GT:AC:AF:NC	0:0:0:A=38,	0:2:0.0769230769231:A=24,C=2,
+phiX174	1298	.	A	C	0	.	AC=3;AF=0.0491803278689	GT:AC:AF:NC	0:3,0:0.0810810810811,0:A=34,C=3,G=1,	0:0,0:0,0:A=24,C=1,T=1,G=1,
+phiX174	1306	.	T	G	0	.	AC=5;AF=0.0943396226415	GT:AC:AF:NC	0:5:0.178571428571:T=23,G=5,	0:0:0:C=1,T=25,
+phiX174	1307	.	T	G	0	.	AC=3;AF=0.0545454545455	GT:AC:AF:NC	0:3:0.107142857143:T=25,G=3,	0:0:0:C=1,T=27,
+phiX174	1314	.	A	G	0	.	AC=5;AF=0.0877192982456	GT:AC:AF:NC	0:2,0:0.0740740740741,0:A=25,C=1,G=2,	0:3,0:0.1,0:A=27,C=1,G=3,
+phiX174	1317	.	A	C	0	.	AC=2;AF=0.0322580645161	GT:AC:AF:NC	0:2:0.0740740740741:A=25,C=2,	0:0:0:A=35,
+phiX174	1320	.	C	G	0	.	AC=2;AF=0.0322580645161	GT:AC:AF:NC	0:2:0.0769230769231:C=24,G=2,	0:0:0:C=36,
+phiX174	1322	.	G	C	0	.	AC=3;AF=0.0441176470588	GT:AC:AF:NC	0:3:0.107142857143:C=3,G=25,	0:0:0:G=40,
+phiX174	1323	.	C	G	0	.	AC=2;AF=0.0298507462687	GT:AC:AF:NC	0:0:0:C=28,	0:2:0.0512820512821:C=37,T=1,G=2,
+phiX174	1329	.	T	C	0	.	AC=2;AF=0.0277777777778	GT:AC:AF:NC	0:2:0.0666666666667:C=2,T=28,	0:0:0:T=42,G=1,
+phiX174	1335	.	C	A	0	.	AC=2;AF=0.025974025974	GT:AC:AF:NC	0:2:0.0625:A=2,C=30,	0:0:0:C=45,
+phiX174	1338	.	T	A	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:0:0:T=32,	0:2:0.047619047619:A=2,T=40,
+phiX174	1345	.	T	C	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:0,0:0,0:T=36,G=1,	0:0,2:0,0.046511627907:C=2,T=41,G=1,
+phiX174	1347	.	A	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0512820512821:A=37,C=2,G=1,	0:0:0:A=43,
+phiX174	1348	.	T	G	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:2:0.05:T=38,G=2,	0:0:0:T=43,
+phiX174	1352	.	A	T	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:0:0:A=34,G=1,	0:2:0.0512820512821:A=37,T=2,
+phiX174	1354	.	T	G,A	0	.	AC=2,2;AF=0.027027027027,0.027027027027	GT:AC:AF:NC	0:2,0:0.0526315789474,0:T=36,G=2,	0:0,2:0,0.0555555555556:A=2,T=34,G=1,
+phiX174	1359	.	T	G	0	.	AC=3;AF=0.0405405405405	GT:AC:AF:NC	0:3:0.0714285714286:T=39,G=3,	0:0:0:T=32,G=1,
+phiX174	1366	.	G	C	0	.	AC=3;AF=0.0428571428571	GT:AC:AF:NC	0:3:0.0714285714286:C=3,T=1,G=39,	0:0:0:G=28,
+phiX174	1370	.	T	G	0	.	AC=2;AF=0.0289855072464	GT:AC:AF:NC	0:0:0:C=1,T=45,G=1,	0:2:0.0833333333333:A=1,T=22,G=2,
+phiX174	1373	.	T	G	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:2:0.0408163265306:T=47,G=2,	0:0:0:T=25,
+phiX174	1380	.	G	C	0	.	AC=2;AF=0.0238095238095	GT:AC:AF:NC	0:0,2:0,0.0384615384615:C=2,T=1,G=50,	0:0,0:0,0:T=1,G=32,
+phiX174	1381	.	T	G	0	.	AC=3;AF=0.0361445783133	GT:AC:AF:NC	0:3:0.0576923076923:A=1,T=49,G=3,	0:0:0:T=31,
+phiX174	1384	.	T	G	0	.	AC=4;AF=0.0512820512821	GT:AC:AF:NC	0:4:0.0816326530612:T=45,G=4,	0:0:0:T=29,G=1,
+phiX174	1385	.	T	G	0	.	AC=4;AF=0.0512820512821	GT:AC:AF:NC	0:4:0.0816326530612:T=45,G=4,	0:0:0:C=1,T=29,
+phiX174	1391	.	A	C	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:2:0.0408163265306:A=47,C=2,	0:0:0:A=30,C=1,
+phiX174	1393	.	C	A	0	.	AC=2;AF=0.0253164556962	GT:AC:AF:NC	0:2:0.0425531914894:A=2,C=45,	0:0:0:C=32,
+phiX174	1396	.	T	G	0	.	AC=3;AF=0.04	GT:AC:AF:NC	0:3:0.0697674418605:T=40,G=3,	0:0:0:T=32,
+phiX174	1397	.	A	C	0	.	AC=2;AF=0.027027027027	GT:AC:AF:NC	0:0:0:A=42,T=1,	0:2:0.0625:A=30,C=2,
+phiX174	1400	.	A	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.047619047619:A=40,C=2,G=1,	0:0:0:A=31,
+phiX174	1401	.	A	C	0	.	AC=2;AF=0.027397260274	GT:AC:AF:NC	0:2:0.047619047619:A=40,C=2,	0:0:0:A=31,
+phiX174	1434	.	C	T	0	.	AC=2;AF=0.0571428571429	GT:AC:AF:NC	0:2:0.142857142857:C=12,T=2,	0:0:0:C=21,
+phiX174	1438	.	G	C	0	.	AC=2;AF=0.0526315789474	GT:AC:AF:NC	0:0:0:G=15,	0:2:0.0869565217391:C=2,G=21,
+phiX174	1450	.	T	G	0	.	AC=3;AF=0.0789473684211	GT:AC:AF:NC	0:3:0.176470588235:A=1,C=1,T=14,G=3,	0:0:0:T=21,G=1,
+phiX174	1459	.	T	G	0	.	AC=3;AF=0.075	GT:AC:AF:NC	0:3:0.142857142857:C=1,T=18,G=3,	0:0:0:T=19,
+phiX174	1470	.	C	A	0	.	AC=2;AF=0.0384615384615	GT:AC:AF:NC	0:0:0:C=29,	0:2:0.0869565217391:A=2,C=21,
+phiX174	1484	.	C	G	0	.	AC=2;AF=0.0384615384615	GT:AC:AF:NC	0:2:0.0740740740741:A=1,C=25,G=2,	0:0:0:C=25,
+phiX174	1487	.	T	G	0	.	AC=2;AF=0.0363636363636	GT:AC:AF:NC	0:2:0.0689655172414:T=27,G=2,	0:0:0:T=26,
+phiX174	1491	.	G	T	0	.	AC=2;AF=0.037037037037	GT:AC:AF:NC	0:0:0:T=1,G=26,	0:2:0.0714285714286:T=2,G=26,
+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,
+phiX174	1603	.	T	G	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0625:T=30,G=2,	0:0:0:T=50,
+phiX174	1606	.	T	G	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0666666666667:A=1,C=1,T=28,G=2,	0:0:0:T=52,
+phiX174	1611	.	A	C	0	.	AC=2;AF=0.0243902439024	GT:AC:AF:NC	0:2:0.0769230769231:A=24,C=2,	0:0:0:A=56,C=1,
+phiX174	1613	.	A	G	0	.	AC=2;AF=0.0240963855422	GT:AC:AF:NC	0:0:0:A=25,C=1,G=1,	0:2:0.0344827586207:A=56,G=2,
+phiX174	1618	.	C	A	0	.	AC=2;AF=0.0229885057471	GT:AC:AF:NC	0:2:0.0666666666667:A=2,C=28,G=1,	0:0:0:A=1,C=57,
+phiX174	1619	.	C	A	0	.	AC=2;AF=0.0229885057471	GT:AC:AF:NC	0:2:0.0666666666667:A=2,C=28,	0:0:0:C=57,
+phiX174	1621	.	A	C	0	.	AC=3;AF=0.0352941176471	GT:AC:AF:NC	0:0:0:A=31,T=1,G=1,	0:3:0.0555555555556:A=51,C=3,
+phiX174	1622	.	G	T	0	.	AC=2;AF=0.0224719101124	GT:AC:AF:NC	0:0:0:A=1,G=35,	0:2:0.037037037037:T=2,G=52,
+phiX174	1624	.	A	G	0	.	AC=2;AF=0.0235294117647	GT:AC:AF:NC	0:2:0.0555555555556:A=34,T=1,G=2,	0:0:0:A=49,
+phiX174	1627	.	T	G,C	0	.	AC=2,2;AF=0.0246913580247,0.0246913580247	GT:AC:AF:NC	0:0,0:0,0:T=37,G=1,	0:2,2:0.0454545454545,0.0454545454545:C=2,T=40,G=2,
+phiX174	1630	.	T	G	0	.	AC=2;AF=0.025641025641	GT:AC:AF:NC	0:2:0.0526315789474:C=1,T=36,G=2,	0:0:0:T=40,
+phiX174	1632	.	A	C	0	.	AC=2;AF=0.0246913580247	GT:AC:AF:NC	0:2:0.05:A=38,C=2,	0:0:0:A=41,
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+phiX174	1942	.	T	G	0	.	AC=2;AF=0.047619047619	GT:AC:AF:NC	0:0:0:T=19,	0:2:0.0869565217391:T=21,G=2,
+phiX174	1945	.	T	G	0	.	AC=3;AF=0.0769230769231	GT:AC:AF:NC	0:0:0:T=15,G=1,	0:3:0.125:T=21,G=3,
+phiX174	1954	.	T	C	0	.	AC=2;AF=0.0625	GT:AC:AF:NC	0:0,0:0,0:T=12,G=1,	0:0,2:0,0.1:C=2,T=18,G=1,
+phiX174	1959	.	T	G	0	.	AC=2;AF=0.0555555555556	GT:AC:AF:NC	0:2:0.153846153846:T=11,G=2,	0:0:0:T=23,
+phiX174	1994	.	A	C	0	.	AC=2;AF=0.0512820512821	GT:AC:AF:NC	0:2:0.153846153846:A=11,C=2,	0:0:0:A=26,
+phiX174	1998	.	A	G	0	.	AC=2;AF=0.05	GT:AC:AF:NC	0:2:0.142857142857:A=12,G=2,	0:0:0:A=26,
diff -r 000000000000 -r b29dbe1270b5 tool-data/fasta_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/fasta_indexes.loc.sample	Thu Mar 19 14:47:59 2015 -0400
@@ -0,0 +1,29 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a fasta_indexes.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The fasta_indexes.loc
+#file has this format (white space characters are TAB characters):
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
+#
+#So, for example, if you had hg19 Canonical indexed stored in
+#
+# /depot/data2/galaxy/hg19/sam/,
+#
+#then the fasta_indexes.loc entry would look like this:
+#
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#
+#and your /depot/data2/galaxy/hg19/sam/ directory
+#would contain hg19canon.fa and hg19canon.fa.fai files.
+#
+#Your fasta_indexes.loc file should include an entry per line for
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
+#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa
diff -r 000000000000 -r b29dbe1270b5 tool-data/tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tool_data_table_conf.xml.sample	Thu Mar 19 14:47:59 2015 -0400
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Location of SAMTools indexes and other files -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>line_type, value, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>
diff -r 000000000000 -r b29dbe1270b5 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Mar 19 14:47:59 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="vcflib" version="8a5602bf07">
+        <repository changeset_revision="7e67466b033e" name="package_vcflib_8a5602bf07" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
diff -r 000000000000 -r b29dbe1270b5 vcfvcfintersect.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfvcfintersect.xml	Thu Mar 19 14:47:59 2015 -0400
@@ -0,0 +1,124 @@
+<tool id="vcfvcfintersect" name="VCF-VCFintersect:" version="0.0.3">
+  <description>Intersect two VCF datasets</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio"></expand>
+  <command>
+
+    #set $reference_fasta_filename = "localref.fa"
+    #if str( $reference_source.reference_source_selector ) == "history":
+       ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+    #else:
+       #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
+    #end if
+    
+    #if $adv_options.adv_options_selector == True:
+    
+    vcfintersect "${adv_options.adv_options_input}" ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}"
+
+    #else:
+
+    vcfintersect ${loci} ${invert} -r "${reference_fasta_filename}" -w "${window_size}" ${isect_union} "${vcf_input1}" "${vcf_input2}" > "${out_file1}"   
+
+    #end if
+
+  </command>
+  <inputs>
+    <!-- selecting refernce source -->
+    <param name="vcf_input1" type="data" format="vcf" label="The first VCF dataset" />
+    <param name="vcf_input2" type="data" format="vcf" label="The second VCF dataset" help="The second dataset will be instersected with the first"/>
+    <conditional name="reference_source">
+      <param name="reference_source_selector" type="select" label="Choose the source for the reference genome" help="This tools needs to access reference genomes sequence specified by this option.">
+	<option value="cached">Locally cached</option>
+	<option value="history">History</option>
+      </param>
+      <when value="cached">
+	<param name="ref_file" type="select" label="Select reference genome">
+	  <options from_data_table="fasta_indexes">
+	    <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
+	  </options>
+	  <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+	</param>
+      </when>
+      <when value="history"> <!-- FIX ME!!!! -->
+	<param name="ref_file" type="data" format="fasta" label="Using reference file" />
+      </when>
+    </conditional>
+    <param name="isect_union" type="select" label="Union or intersection" help="-i or -u">
+      <option value="-i">Intersect</option>
+      <option value="-u">Union</option>
+    </param>
+    <param name="invert" type="boolean" truevalue="-v" falsevalue="" label="Invert selection?" help="-v, --invert" />
+    <param name="window_size" type="integer" value="30" label="compare records up to this many bp away (window size)" help="-w, --window-size" />
+    <param name="loci" type="boolean" truevalue="-l" falsevalue="" label="output whole loci when one alternate allele matches" help="-l, --loci" />
+    <conditional name="adv_options">
+      <param name="adv_options_selector" type="boolean" truevalue="use_adv_controls" label="Advanced controls" help="Allows you to specify options that are not listed above"/> 
+      <when value="use_adv_controls">
+	<param name="adv_options_input" type="text" value="-t &quot;vcfvcf-intersect-result&quot;" label="Enter additional command line options described in the help section below" help="such as -m, -t, -V, -M, and -T" />
+	<sanitizer>
+	  <valid initial="string.printable">
+	    <remove value="&apos;"/>
+	  </valid>
+	  <mapping initial="none">
+	    <add source="&apos;" target="__sq__"/>
+	  </mapping>
+	</sanitizer>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="reference_source_selector" value="history" />
+      <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />
+      <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" />
+      <param name="isect_union" value="-i" />
+      <param name="invert" value="False" />
+      <param name="loci" value="False" />
+      <patam name="adv_options" value="False" />
+      <param name="window_size" value="30" />
+      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
+      <output name="out_file1" file="vcfvcfintersect-test1.vcf"/>
+    </test>
+    <test>
+      <param name="reference_source_selector" value="history" />
+      <param name="vcf_input1" value="vcfvcfintersect-input1.vcf" />
+      <param name="vcf_input2" value="vcfvcfintersect-input2.vcf" />
+      <param name="isect_union" value="-u" />
+      <param name="invert" value="False" />
+      <param name="loci" value="False" />
+      <patam name="adv_options" value="False" />
+      <param name="window_size" value="30" />
+      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
+      <output name="out_file1" file="vcfvcfintersect-test2.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+Computes intersections and unions for two VCF datasets. Unifies equivalent alleles within window-size bp. 
+
+The options are::
+
+    -v, --invert              invert the selection, printing only records which would
+    -i, --intersect-vcf FILE  use this VCF for set intersection generation
+    -u, --union-vcf FILE      use this VCF for set union generation
+    -w, --window-size N       compare records up to this many bp away (default 30)
+    -l, --loci                output whole loci when one alternate allele matches
+    -m, --ref-match           intersect on the basis of record REF string
+    -t, --tag TAG             attach TAG to each record's info field if it would intersect
+    -V, --tag-value VAL       use this value to indicate that the allele is passing
+                              '.' will be used otherwise.  default: 'PASS'
+    -M, --merge-from FROM-TAG
+    -T, --merge-to   TO-TAG   merge from FROM-TAG used in the -i file, setting TO-TAG
+                              in the current file.
+
+----
+
+VCFVCFintersect is based on vcfintersect utility of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
+</help>
+  <expand macro="citations" />
+</tool>