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changeset 2:aa3ca755f70d draft

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Uploaded
author anton
date Wed, 11 Jun 2014 16:16:43 -0400
parents 551d94c28e3b
children 1a28e1ddcd99
files test-data/vcfgeno2haplo-test1.vcf test-data/vcflib-phix.vcf test-data/vcflib-test-genome-phix.fa tool_dependencies.xml vcfgeno2haplo.xml
diffstat 5 files changed, 238 insertions(+), 34 deletions(-) [+]
line wrap: on
line diff
--- a/test-data/vcfgeno2haplo-test1.vcf	Tue Jun 10 12:37:48 2014 -0400
+++ b/test-data/vcfgeno2haplo-test1.vcf	Wed Jun 11 16:16:43 2014 -0400
@@ -1,29 +1,12 @@
-##fileformat=VCFv4.0
-##fileDate=20090805
-##source=myImputationProgramV3.1
-##reference=1000GenomesPilot-NCBI36
-##phasing=partial
-##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
-##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
-##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
-##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
-##FILTER=<ID=q10,Description="Quality below 10">
-##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##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=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
-##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
-##ALT=<ID=CNV,Description="Copy number variable region">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
-20	14370	rs6054257	G	A	29	PASS	AF=0.5;DP=14;NS=3;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
-20	17330	.	T	A	3	q10	AF=0.017;DP=11;NS=3	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:.,.
-20	1110696	rs6040355	A	G,T	67	PASS	AA=T;AF=0.333,0.667;DP=10;NS=2;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:.,.
-20	1230237	.	T	.	47	PASS	AA=T;DP=13;NS=3	GT:GQ:DP:HQ	0|0:54:.:56,60	0|0:48:4:51,51	0/0:61:2:.,.
-20	1234567	microsat1	G	GA,GAC	50	PASS	AA=G;AC=3,1;AN=6;DP=9;NS=3	GT:GQ:DP	0/1:.:4	0/2:17:2	1/1:40:3
-20	1235237	.	T	.	0	.	.	GT	0/0	0|0	.
-X	10	rsTest	AC	A,ATG	10	PASS	.	GT	0	0/1	0|2
+##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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcflib-phix.vcf	Wed Jun 11 16:16:43 2014 -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,
+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,
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/vcflib-test-genome-phix.fa	Wed Jun 11 16:16:43 2014 -0400
@@ -0,0 +1,2 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
--- a/tool_dependencies.xml	Tue Jun 10 12:37:48 2014 -0400
+++ b/tool_dependencies.xml	Wed Jun 11 16:16:43 2014 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="vcflib" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">
-        <repository changeset_revision="3d515e915297" name="package_vcflib" owner="anton" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="3d515e915297" name="package_vcflib" owner="anton" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
--- a/vcfgeno2haplo.xml	Tue Jun 10 12:37:48 2014 -0400
+++ b/vcfgeno2haplo.xml	Wed Jun 11 16:16:43 2014 -0400
@@ -10,7 +10,7 @@
     #else:
        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if    
-  vcfgeno2haplo "${output_option}" -w "${window_size}" -r "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
+  vcfgeno2haplo ${output_option} -w ${window_size} -r "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
   <inputs>
     <conditional name="reference_source">
        <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
@@ -37,7 +37,7 @@
        </when>
      </conditional>
      <param name="window_size" type="text" size="4" value="30" label="compare records up to this many bp away (window size)" help="--window-size option (default = 30)" />
-     <param name="output_option" type="boolean" truevalue="-o" label="What to report?" help="--only-variants option" />
+     <param name="output_option" type="boolean" truevalue="-o" falsevalue="" label="What to report?" help="--only-variants option" />
 <!--       <option value=" ">Output entire haplotype</option>
        <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by &quot;:&quot;)</option>
      </param> -->
@@ -52,9 +52,9 @@
     <test>
       <param name="reference_source_selector" value="history" />
       <param name="output_option" value="true" />
-      <param name="window_size" value="10000" />
-      <param name="input_vcf" value="vcflib-chr20-X.vcf"/>
-      <param name="ref_file" value="vcflib-human-reference-chr20-XY.fa" />
+      <param name="window_size" value="5000" />
+      <param name="input_vcf" value="vcflib-phix.vcf"/>
+      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
       <output name="out_file1" file="vcfgeno2haplo-test1.vcf"/>
     </test>
     </tests>