ngs_server 0.1 → 0.2

data/ext/vcftools/examples/.svn/prop-base/perl-api-1.pl.svn-base

@@ -0,0 +1,5 @@
+K 14
+svn:executable
+V 1
+*
+END

data/ext/vcftools/examples/.svn/text-base/annotate-test.vcf.svn-base

@@ -0,0 +1,37 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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">
+##FILTER=<ID=q10,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	100	.	GTTT	G	1806	q10	DP=35
+1	104	.	C	.	1792	PASS	DP=32
+1	105	.	C	T	246	PASS	DP=10
+1	106	.	C	A	246	PASS	DP=10
+2	107	.	C	.	1806	q10	DP=35
+2	108	.	C	.	1792	PASS	DP=32
+2	109	.	C	.	628	q10	DP=21
+2	110	.	C	G	1016	PASS	DP=22
+2	111	.	C	G	727	PASS	DP=30
+2	112	.	C	G	246	PASS	DP=10
+2	113	.	C	.	246	PASS	DP=10
+2	114	.	T	.	246	PASS	DP=10
+2	115	.	T	.	246	PASS	DP=10
+2	116	.	T	.	246	PASS	DP=10
+2	117	.	T	A	246	PASS	DP=10
+2	118	.	T	C	246	PASS	DP=10
+2	119	.	TAAA	T	246	PASS	DP=10
+2	124	.	TA	T	246	PASS	DP=10
+2	128	.	T	TA	246	PASS	DP=10
+2	130	.	C 	A	246	PASS	DP=10
+2	131	.	T	A	246	PASS	DP=10
+2	132	.	T	A	246	PASS	DP=10
+2	133	.	T	A	246	PASS	DP=10
+2	134	.	T	A	246	PASS	DP=10
+2	135	.	T	C	246	PASS	DP=10
+2	136	.	TT	T	246	PASS	DP=10
+17	12412	.	CAGAGAGAGA	CAGAGAGAGAGA	74.8	.	INDEL;DP=5388;AF1=0.006576;CI95=0.005525,0.01105;DP4=2077,2367,21,22;MQ=47;FQ=74.8;PV4=0.88,1,0.34,0.021
+17	12427	.	G	A	999	.	DP=5557;AF1=0.06028;CI95=0.04972,0.07182;DP4=2461,2689,106,74;MQ=47;FQ=999;PV4=0.0038,1,2.6e-12,1
+17	69284	.	G	A	14.6	.	DP=3946;AF1=0.003468;CI95=0.002762,0.008287;DP4=1529,2177,7,9;MQ=44;FQ=14.6;PV4=1,0.035,0.098,1
+17	69293	.	GTTTCATTTC	GTTTCTTTTCATTTC	999	.	INDEL;DP=3568;AF1=0.1295;CI95=0.1077,0.1547;DP4=1014,1238,118,121;MQ=44;FQ=999;PV4=0.22,1,9.4e-54,1

data/ext/vcftools/examples/.svn/text-base/annotate.out.svn-base

@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##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">
+##FILTER=<ID=q10,Description="Quality below 10">
+##INFO=<ID=HM2,Number=0,Type=Flag,Description="HapMap2 membership">
+##INFO=<ID=GN,Number=1,Type=String,Description="Gene Name">
+##INFO=<ID=DP,Number=0,Type=Integer,Description="Depth,etc">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	100	.	GTTT	G	1806	q10	DP=5;GN=gene1;HM2	GT:GQ:DP	0/1:409:35
+1	110	.	CAAA	C	1792	PASS	DP=6	GT:GQ:DP	0/1:245:32
+1	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	130	.	GAA	G	1016	PASS	DP=7;HM2	GT:GQ:DP	0/1:212:22
+1	140	.	GT	G	727	PASS	DP=8	GT:GQ:DP	0/1:150:30
+1	150	.	TAAAA	TA,T	246	PASS	DP=9	GT:GQ:DP	1/2:12:10
+1	160	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	100	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+2	110	.	CAAA	C	1792	PASS	GN=gene2;HM2	GT:GQ:DP	0/1:245:32
+2	120	.	GA	G	628	q10	GN=gene2;HM2	GT:GQ:DP	1/1:21:21
+2	130	.	GAA	G	1016	PASS	GN=gene2;HM2	GT:GQ:DP	0/1:212:22
+2	140	.	GT	G	727	PASS	GN=gene2;HM2	GT:GQ:DP	0/1:150:30
+2	150	.	TAAAA	TA,T	246	PASS	GN=gene2;HM2	GT:GQ:DP	1/2:12:10
+2	160	.	TAAAA	TA,TC,T	246	PASS	DP=11;GN=gene3	GT:GQ:DP	0/2:12:10

data/ext/vcftools/examples/.svn/text-base/annotate.txt.svn-base

@@ -0,0 +1,7 @@
+100	100	1	id1_100	.	.	HM2	gene1	5
+110	110	1	id1_110	CAAA	C	0	.	6
+130	130	1	id1_130	GAA	GG	HM2	.	7
+140	140	1	id1_140	GT	G	0	.	8
+150	150	1	id1_150	TAAAA	T	0	.	9
+110	150	2	id2_110_150	CAAA	C	HM2	gene2	.
+160	160	2	id2_160	TAAAA	TC	0	gene3	11

data/ext/vcftools/examples/.svn/text-base/annotate2.out.svn-base

@@ -0,0 +1,52 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=SnpCluster,Description="Filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases [win=3,count=2]">
+##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]">
+##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
+##FILTER=<ID=MaxDP,Description="Maximum read depth (INFO/DP or INFO/DP4) [34]">
+##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [0]">
+##FILTER=<ID=MinMQ,Description="Minimum RMS mapping quality for SNPs (INFO/MQ) [10]">
+##FILTER=<ID=Qual,Description="Minimum value of the QUAL field [10]">
+##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
+##FILTER=<ID=VDB,Description="Minimum Variant Distance Bias (INFO/VDB) [0.015]">
+##FILTER=<ID=GapWin,Description="Window size for filtering adjacent gaps [3]">
+##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">
+##FILTER=<ID=SnpGap,Description="SNP within INT bp around a gap to be filtered [10]">
+##FILTER=<ID=MinDP,Description="Minimum read depth (INFO/DP or INFO/DP4) [2]">
+##FILTER=<ID=RefN,Description="Reference base is N []">
+##FILTER=<ID=HWE,Description="Minimum P-value for HWE (plus F<0) (INFO/HWE and INFO/G3) [0.0001]">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	100	.	GTTT	G	1806	q10;MaxDP	DP=35
+1	104	.	C	.	1792	PASS	DP=32
+1	105	.	C	T	246	SnpGap;SnpCluster	DP=10
+1	106	.	C	A	246	SnpGap;SnpCluster	DP=10
+2	107	.	C	.	1806	q10;MaxDP	DP=35
+2	108	.	C	.	1792	PASS	DP=32
+2	109	.	C	.	628	q10	DP=21
+2	110	.	C	G	1016	SnpGap;SnpCluster	DP=22
+2	111	.	C	G	727	SnpGap;SnpCluster	DP=30
+2	112	.	C	G	246	SnpGap;SnpCluster	DP=10
+2	113	.	C	.	246	PASS	DP=10
+2	114	.	T	.	246	PASS	DP=10
+2	115	.	T	.	246	PASS	DP=10
+2	116	.	T	.	246	PASS	DP=10
+2	117	.	T	A	246	SnpGap;SnpCluster	DP=10
+2	118	.	T	C	246	SnpGap;SnpCluster	DP=10
+2	119	.	TAAA	T	246	GapWin;SnpCluster	DP=10
+2	124	.	TA	T	246	GapWin	DP=10
+2	128	.	T	TA	246	SnpCluster	DP=10
+2	130	.	C 	A	246	SnpGap;SnpCluster	DP=10
+2	131	.	T	A	246	SnpGap;SnpCluster	DP=10
+2	132	.	T	A	246	SnpGap;SnpCluster	DP=10
+2	133	.	T	A	246	SnpGap;SnpCluster	DP=10
+2	134	.	T	A	246	SnpGap;SnpCluster	DP=10
+2	135	.	T	C	246	SnpGap;SnpCluster	DP=10
+2	136	.	TT	T	246	SnpCluster	DP=10
+17	12412	.	CAGAGAGAGA	CAGAGAGAGAGA	74.8	MaxDP	INDEL;DP=5388;AF1=0.006576;CI95=0.005525,0.01105;DP4=2077,2367,21,22;MQ=47;FQ=74.8;PV4=0.88,1,0.34,0.021
+17	12427	.	G	A	999	MaxDP;SnpGap	DP=5557;AF1=0.06028;CI95=0.04972,0.07182;DP4=2461,2689,106,74;MQ=47;FQ=999;PV4=0.0038,1,2.6e-12,1
+17	69284	.	G	A	14.6	MaxDP;SnpGap	DP=3946;AF1=0.003468;CI95=0.002762,0.008287;DP4=1529,2177,7,9;MQ=44;FQ=14.6;PV4=1,0.035,0.098,1
+17	69293	.	GTTTCATTTC	GTTTCTTTTCATTTC	999	MaxDP	INDEL;DP=3568;AF1=0.1295;CI95=0.1077,0.1547;DP4=1014,1238,118,121;MQ=44;FQ=999;PV4=0.22,1,9.4e-54,1

data/ext/vcftools/examples/.svn/text-base/annotate3.out.svn-base

@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##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">
+##FILTER=<ID=q10,Description="Quality below 10">
+##INFO=<ID=HM2,Number=0,Type=Flag,Description="HapMap2 membership">
+##INFO=<ID=GN,Number=1,Type=String,Description="Gene Name">
+##INFO=<ID=DP,Number=0,Type=Integer,Description="Depth,etc">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	100	id1_100	GTTT	G	1806	q10	DP=5;GN=gene1;HM2	GT:GQ:DP	0/1:409:35
+1	110	id1_110	CAAA	C	1792	PASS	DP=6	GT:GQ:DP	0/1:245:32
+1	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	140	id1_140	GT	G	727	PASS	DP=8	GT:GQ:DP	0/1:150:30
+1	150	id1_150	TAAAA	TA,T	246	PASS	DP=9	GT:GQ:DP	1/2:12:10
+1	160	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	100	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+2	110	id2_110_150	CAAA	C	1792	PASS	GN=gene2;HM2	GT:GQ:DP	0/1:245:32
+2	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+2	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+2	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+2	150	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	160	id2_160	TAAAA	TA,TC,T	246	PASS	DP=11;GN=gene3	GT:GQ:DP	0/2:12:10

data/ext/vcftools/examples/.svn/text-base/cmp-test-a-3.3.vcf.svn-base

@@ -0,0 +1,12 @@
+##fileformat=VCFv3.3
+##INFO=DP,1,Integer,"Total Depth"
+##FORMAT=GT,1,String,"Genotype"
+##FORMAT=GQ,1,Integer,"Genotype Quality"
+##FORMAT=DP,1,Integer,"Read Depth"
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	100100	.	G	C	0	.	DP=1	GT:GQ:DP	0|1:40:1	0/1:40:1
+1	100200	.	G	C	0	.	DP=1	GT:GQ:DP	0|1:40:1	0/0:40:1
+1	100300	.	G	C	0	.	DP=1	GT:GQ:DP	1/1:40:1	./.:40:1
+1	100400	.	C	G,T	35	.	DP=1	GT:GQ:DP	1/1:41:1	0/2:40:1
+1	100500	.	A	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1
+1	100600	.	C	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1

data/ext/vcftools/examples/.svn/text-base/cmp-test-a.vcf.svn-base

@@ -0,0 +1,12 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	100100	.	G	C	0	.	DP=1	GT:GQ:DP	0|1:40:1	0/1:40:1
+1	100200	.	G	C	0	.	DP=1	GT:GQ:DP	0|1:40:1	0/0:40:1
+1	100300	.	G	C	0	.	DP=1	GT:GQ:DP	1/1:40:1	./.:40:1
+1	100400	.	C	G,T	35	.	DP=1	GT:GQ:DP	1/1:41:1	0/2:40:1
+1	100500	.	A	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1
+1	100600	.	C	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1

data/ext/vcftools/examples/.svn/text-base/cmp-test-b-3.3.vcf.svn-base

@@ -0,0 +1,12 @@
+##fileformat=VCFv3.3
+##INFO=DP,1,Integer,"Total Depth"
+##FORMAT=GT,1,String,"Genotype"
+##FORMAT=GQ,1,Integer,"Genotype Quality"
+##FORMAT=DP,1,Integer,"Read Depth"
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	100100	.	G	C	0	.	DP=1	GT:GQ:DP	0|1:40:1	1/0:40:1
+1	100200	.	G	C	0	.	DP=1	GT:GQ:DP	1|0:40:1	0/0:40:1
+1	100300	.	G	C	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1
+1	100400	.	C	G	35	.	DP=1	GT:GQ:DP	1/1:41:1	0/0:40:1
+1	100500	.	A	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1
+1	100600	.	C	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1

data/ext/vcftools/examples/.svn/text-base/cmp-test-b.vcf.svn-base

@@ -0,0 +1,12 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	100100	.	G	C	0	.	DP=1	GT:GQ:DP	0|1:40:1	1/0:40:1
+1	100200	.	G	C	0	.	DP=1	GT:GQ:DP	1|0:40:1	0/0:40:1
+1	100300	.	G	C	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1
+1	100400	.	C	G	35	.	DP=1	GT:GQ:DP	1/1:41:1	0/0:40:1
+1	100500	.	A	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1
+1	100600	.	C	G	0	.	DP=1	GT:GQ:DP	1/1:40:1	0/0:40:1

data/ext/vcftools/examples/.svn/text-base/cmp-test.out.svn-base

@@ -0,0 +1,53 @@
+# This file was generated by vcf-compare.
+#
+#VN 'Venn-Diagram Numbers'. Use `grep ^VN | cut -f 2-` to extract this part.
+#VN The columns are: 
+#VN        1  .. number of sites unique to this particular combination of files
+#VN        2- .. combination of files and space-separated number, a fraction of sites in the file
+VN	6	cmp-test-a.vcf.gz (100.0%)	cmp-test-b.vcf.gz (100.0%)
+#SN Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
+SN	Number of REF matches:	6
+SN	Number of ALT matches:	5
+SN	Number of REF mismatches:	0
+SN	Number of ALT mismatches:	1
+SN	Number of samples in GT comparison:	2
+#GS Genotype Comparison Summary. Use `grep ^GS | cut -f 2-` to extract this part.
+#GS The columns are:
+#GS        1  .. variant type
+#GS        2  .. number of mismatches
+#GS        3  .. number of matches
+#GS        4  .. discordance
+GS	hom_RR	0	3	0.00%
+GS	het_RA	1	3	25.00%
+GS	hom_AA	0	4	0.00%
+GS	het_AA	0	0	0.00%
+SN	Non-reference Discordance Rate (NDR):	12.50
+
+#GC Genotype Comparison. Use `grep ^GC | cut -f 2-` to extract this part.
+#GC The columns are:
+#GC       1     .. Sample
+#GC       2-6   .. Gtype mismatches: total hom_RR hom_AA het_RA het_AA 
+#GC       7-9   .. Gtype lost: total het_RA het_AA 
+#GC       10-14 .. Gtype gained: total hom_RR hom_AA het_RA het_AA 
+#GC       15-17 .. Phase lost: total het_RA het_AA 
+#GC       18    .. Phase gained
+#GC       19-23 .. Matching sites: total hom_RR hom_AA het_RA het_AA 
+#GC       24-26 .. Phased matches: total het_RA het_AA 
+#GC       27-29 .. Misphased matches: total het_RA het_AA 
+GC	A	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	4	2	0	1	1	0	0	0	0
+GC	B	1	0	0	1	0	0	0	0	1	1	0	0	0	0	0	0	0	4	3	0	1	0	0	0	0	0	0	0
+#FC Genotype Concordance vs non-ref allele frequency. Use `^FC | cut -f 2-` to extract this part.
+#FC The columns are:
+#FC      1  .. Non-ref allele count
+#FC      2  .. Hom(RR) concordance
+#FC      3  .. Het(RA) concordance
+#FC      4  .. Hom(AA) concordance
+#FC      5  .. Het(AA) concordance
+#FC      6  .. Number of Hom(RR) gtypes
+#FC      7  .. Number of Het(RA) gtypes
+#FC      8  .. Number of Hom(AA) gtypes
+#FC      9  .. Number of Het(AA) gtypes
+FC	0.25	1.000	1.000	-1.000	-1.000	1	1	0	0
+FC	0.50	1.000	1.000	1.000	-1.000	2	2	2	0
+FC	0.75	-1.000	0.000	1.000	-1.000	0	1	1	0
+FC	1.00	-1.000	-1.000	1.000	-1.000	0	0	1	0

data/ext/vcftools/examples/.svn/text-base/concat-a.vcf.svn-base

@@ -0,0 +1,21 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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">
+##FILTER=<ID=q10,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	100	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+1	110	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+1	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+1	150	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+1	160	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	100	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+2	110	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+2	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+2	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+2	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+2	150	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	160	.	TAAAA	TA,TC,T	246	PASS	DP=10	GT:GQ:DP	0/2:12:10

data/ext/vcftools/examples/.svn/text-base/concat-b.vcf.svn-base

@@ -0,0 +1,13 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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">
+##FILTER=<ID=q10,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	141	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+1	151	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+1	161	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	171	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	181	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+1	191	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10

data/ext/vcftools/examples/.svn/text-base/concat-c.vcf.svn-base

@@ -0,0 +1,19 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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">
+##FILTER=<ID=q10,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+2	142	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+2	152	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+2	162	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+2	172	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+2	182	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+2	192	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+1	142	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+1	152	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+1	162	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	172	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	182	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+1	192	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10

data/ext/vcftools/examples/.svn/text-base/concat.out.svn-base

@@ -0,0 +1,39 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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">
+##FILTER=<ID=q10,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	100	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+1	110	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+1	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+1	141	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+1	142	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+1	150	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+1	151	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+1	152	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+1	160	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+1	161	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	162	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	171	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	172	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	181	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+1	182	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+1	191	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+1	192	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	100	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+2	110	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+2	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+2	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+2	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+2	142	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+2	150	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	152	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+2	160	.	TAAAA	TA,TC,T	246	PASS	DP=10	GT:GQ:DP	0/2:12:10
+2	162	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+2	172	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+2	182	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+2	192	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10

data/ext/vcftools/examples/.svn/text-base/invalid-4.0.vcf.svn-base

@@ -0,0 +1,31 @@
+##fileformat=VCFv4.0
+##problem1=The first base of the second ALT allele at 20:1234567 does not match the reference.
+##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=-1,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=-1,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">
+##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">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+19	111	.	A	C	9.6	.	.	GT:HQ	0|0:10,10	0|0:10,10	0\1:3,3
+19	112	.	A	G	10	.	.	GT:HQ	0|0:10,10	0|0:10,10	0\1:3,3
+20	14370	rs6054257	G	A	29	0	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:-1,-1
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:-1,-1
+20	1110696	rs6040355	A	G,T	67	0	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ	1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:-1,-1
+20	1230237	.	T	.	47	0	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:-1:56,60	0|0:48:4:51,51	0/0:61:2:-1,-1
+20	1234567	microsat1	G	GA,AAC	50	0	NS=3;DP=9;AA=G;AN=6;AC=3,1	GT:GQ:DP	0/1:-1:4	0/2:17:2	1/1:40:3
+20	1235237	.	T	.	-1	.	.	GT	0\0	0|0	./.
+X	10	rsTest	AC	A,ATG	10	.	.	GT	0	0/1	0|2
+X	11	rsTest2	T	A,G	10	q10;s50	.	GT:DP:GQ	0:3:10	.:5:20	0:3:10

data/ext/vcftools/examples/.svn/text-base/isec-n2-test.vcf.out.svn-base

@@ -0,0 +1,19 @@
+Warning: The column names do not match (e.g. B):
+B
+A
+##fileformat=VCFv4.0
+##FILTER=<ID=q10,Description="Quality below 10">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
+##FILTER=<ID=q20,Description="Mapping quality below 20">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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">
+##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	3062915	.	GTTT	G	1806	q10	DP=35;SF=0f,1f,2	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20
+1	3106154	.	CAAA	C	1792	PASS	DP=32;SF=0,1,2	GT:GQ:DP	0/1:245:32
+1	3157410	.	GA	G	628	q10	DP=21;SF=0f,1,2	GT:GQ:DP	1/1:21:21
+1	3162006	.	GAA	G	1016	PASS	DP=22;SF=0,1,2	GT:GQ:DP	0/1:212:22
+1	3177144	.	GT	G	727	PASS	DP=30;SF=0,1,2	GT:GQ:DP	0/1:150:30
+1	3184885	.	TAAAA	TA,T	246	PASS	DP=10;SF=0,1	GT:GQ:DP	1/2:12:10

data/ext/vcftools/examples/.svn/text-base/merge-test-a.vcf.svn-base

@@ -0,0 +1,17 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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=GL,Number=G,Type=Float,Description="Genotype Likelihood">
+##FILTER=<ID=q10,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	3062915	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20
+1	3106154	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+1	3157410	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+1	3162006	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+1	3177144	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+1	3184885	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	3199812	.	G	GTT,GT	481	PASS	DP=26	GT:GQ:DP	1/2:322:26
+3	3212016	.	CTT	C,CT	565	PASS	DP=26	GT:GQ:DP	1/2:91:26
+4	3258448	.	TACACACAC	T	325	PASS	DP=31	GT:GQ:DP	0/1:325:31

data/ext/vcftools/examples/.svn/text-base/merge-test-b.vcf.svn-base

@@ -0,0 +1,17 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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=GL,Number=G,Type=Float,Description="Genotype Likelihood">
+##FILTER=<ID=q20,Description="Mapping quality below 20">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	B
+1	3062915	.	GTTT	GT	376	q20	DP=14	GT:GQ:DP:GL	0/1:376:14:-10,0,-10
+1	3106154	.	CAAAA	C	677	PASS	DP=15	GT:GQ:DP:GL	0/1:277:15:-10,0,-10
+1	3157410	.	GA	G	249	PASS	DP=11	GT:GQ:DP	0/1:49:11
+1	3162006	.	GAA	G	663	PASS	DP=19	GT:GQ:DP	0/1:589:19
+1	3177144	.	GT	G	460	PASS	DP=24	GT:GQ:DP	0/1:236:24
+1	3184885	.	TAAA	T	598	PASS	DP=16	GT:GQ:DP	0/1:435:16
+2	3188209	.	GA	G	162	.	DP=15	GT:GQ:DP	0/1:162:15
+3	3199812	.	G	GTT,GT	353	PASS	DP=19	GT:GQ:DP	1/2:188:19
+4	3212016	.	CTT	C	677	q20	DP=15	GT:GQ:DP	0/1:158:15

data/ext/vcftools/examples/.svn/text-base/merge-test-c.vcf.svn-base

@@ -0,0 +1,15 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	C
+1	3062915	.	GTTT	G	388	.	DP=10	GT:GQ:DP	0/1:149:10
+1	3106154	.	CAAA	C	269	.	DP=9	GT:GQ:DP	1/1:25:9
+1	3157410	.	GA	G	212	.	DP=10	GT:GQ:DP	0/1:52:10
+1	3162006	.	GAA	G	558	.	DP=17	GT:GQ:DP	0/1:163:17
+1	3177144	.	GT	G	211	.	DP=14	GT:GQ:DP	0/1:151:14
+1	3199812	.	G	GT	.	.	.	GT	1/1
+2	3212016	.	CTT	C	613	.	DP=11	GT:GQ:DP	0/1:41:11
+3	3242491	.	TT	T	.	.	.	GT	1/1
+4	3291771	.	T	TAA,TAAA	336	.	DP=12	GT:GQ:DP	1/2:2:12

data/ext/vcftools/examples/.svn/text-base/merge-test.vcf.out.svn-base

@@ -0,0 +1,31 @@
+Using column name 'A' for merge-test-a.vcf.gz:A
+Using column name 'B' for merge-test-b.vcf.gz:B
+Using column name 'C' for merge-test-c.vcf.gz:C
+##fileformat=VCFv4.1
+##FILTER=<ID=q10,Description="Quality below 10">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
+##FILTER=<ID=q20,Description="Mapping quality below 20">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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">
+##INFO=<ID=SF,Number=.,Type=String,Description="Source File (index to sourceFiles, f when filtered)">
+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	C
+1	3062915	.	GTTT	G,GT	856.67	q20;q10	AC=2,1;AN=6;DP=35;SF=0f,1f,2	GT:GL:DP:GQ	0/1:-20,-5,-20,.,.,.:35:409	0/2:-10,.,.,0,.,-10:14:376	0/1:.:10:149
+1	3106154	.	CAAAA	CA,C	912.67	PASS	AC=3,1;AN=6;DP=32;SF=0,1,2	GT:GL:DP:GQ	0/1:.:32:245	0/2:-10,.,.,0,.,-10:15:277	1/1:.:9:25
+1	3157410	.	GA	G	363.00	q10	AC=4;AN=6;DP=21;SF=0f,1,2	GT:DP:GQ	1/1:21:21	0/1:11:49	0/1:10:52
+1	3162006	.	GAA	G	745.67	PASS	AC=3;AN=6;DP=22;SF=0,1,2	GT:DP:GQ	0/1:22:212	0/1:19:589	0/1:17:163
+1	3177144	.	GT	G	466.00	PASS	AC=3;AN=6;DP=30;SF=0,1,2	GT:DP:GQ	0/1:30:150	0/1:24:236	0/1:14:151
+1	3184885	.	TAAAA	TA,T	422.00	PASS	AC=2,1;AN=4;DP=10;SF=0,1	GT:DP:GQ	1/2:10:12	0/1:16:435	.
+1	3199812	.	G	GT	.	.	AC=2;AN=2;SF=2	GT	.	.	1/1
+2	3188209	.	GA	G	162.00	.	AC=1;AN=2;DP=15;SF=1	GT:DP:GQ	.	0/1:15:162	.
+2	3199812	.	G	GTT,GT	481.00	PASS	AC=1,1;AN=2;DP=26;SF=0	GT:DP:GQ	1/2:26:322	.	.
+2	3212016	.	CTT	C	613.00	.	AC=1;AN=2;DP=11;SF=2	GT:DP:GQ	.	.	0/1:11:41
+3	3199812	.	G	GTT,GT	353.00	PASS	AC=1,1;AN=2;DP=19;SF=1	GT:DP:GQ	.	1/2:19:188	.
+3	3212016	.	CTT	C,CT	565.00	PASS	AC=1,1;AN=2;DP=26;SF=0	GT:DP:GQ	1/2:26:91	.	.
+3	3242491	.	TT	T	.	.	AC=2;AN=2;SF=2	GT	.	.	1/1
+4	3212016	.	CTT	C	677.00	q20	AC=1;AN=2;DP=15;SF=1f	GT:DP:GQ	.	0/1:15:158	.
+4	3258448	.	TACACACAC	T	325.00	PASS	AC=1;AN=2;DP=31;SF=0	GT:DP:GQ	0/1:31:325	.	.
+4	3291771	.	T	TAA,TAAA	336.00	.	AC=1,1;AN=2;DP=12;SF=2	GT:DP:GQ	.	.	1/2:12:2

data/ext/vcftools/examples/.svn/text-base/perl-api-1.pl.svn-base

@@ -0,0 +1,46 @@
+#!/usr/bin/env perl
+#
+# Example code for generating a minimal VCF file using the perl API
+#
+# Author: pd3@sanger
+#
+
+use strict;
+use warnings;
+use Carp;
+use Vcf;
+
+my $sample = 'Sample1';
+my $vcf_out = Vcf->new();
+$vcf_out->add_columns($sample);
+$vcf_out->add_header_line({key=>'FORMAT',ID=>'GT',Number=>'1',Type=>'String',Description=>"Genotype"});
+$vcf_out->add_header_line({key=>'ALT',ID=>'DEL',Description=>"Deletion"});
+$vcf_out->add_header_line({key=>'ALT',ID=>'DEL:ME:ALU',Description=>"Deletion of ALU element"});
+$vcf_out->add_header_line({key=>'ALT',ID=>'DEL:ME:L1',Description=>"Deletion of L1 element"});
+$vcf_out->add_header_line({key=>'ALT',ID=>'DUP',Description=>"Duplication"});
+$vcf_out->add_header_line({key=>'INFO',ID=>'DP',Number=>1,Type=>'Integer',Description=>"Total Depth"});
+$vcf_out->add_header_line({key=>'INFO',ID=>'H2',Number=>0,Type=>'Flag',Description=>"HapMap2 membership"});
+
+print $vcf_out->format_header();
+
+my $pos = 1;
+for my $gt qw(A/A C/C <DEL>/C <DEL:ME:ALU>/<DEL:ME:ALU> <DEL:ME:L1>/<DEL:ME:L1> <DUP>/<DUP>)
+{
+    $pos++;
+
+    my %out;
+    $out{CHROM}  = '1';
+    $out{POS}    = $pos;
+    $out{ID}     = '.';
+    $out{ALT}    = [];
+    $out{REF}    = 'C';
+    $out{QUAL}   = '.';
+    $out{FILTER} = ['.'];
+    $out{INFO}   = { DP=>3, H2=>undef };
+    $out{FORMAT} = ['GT'];
+    $out{gtypes}{$sample}{GT} = $gt;
+
+    $vcf_out->format_genotype_strings(\%out);
+    print $vcf_out->format_line(\%out);
+}
+

data/ext/vcftools/examples/.svn/text-base/query-test.out.svn-base

@@ -0,0 +1,6 @@
+1:100100	ref=G	alt=C	qual=0	1	A=G|C	B=G/C
+1:100200	ref=G	alt=C	qual=0	1	A=G|C	B=G/G
+1:100300	ref=G	alt=C	qual=0	1	A=C/C	B=./.
+1:100400	ref=C	alt=G,T	qual=35	1	A=G/G	B=C/T
+1:100500	ref=A	alt=G	qual=0	1	A=G/G	B=A/A
+1:100600	ref=C	alt=G	qual=0	1	A=G/G	B=C/C

data/ext/vcftools/examples/.svn/text-base/shuffle-test.vcf.svn-base

@@ -0,0 +1,12 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	B	A
+1	100100	.	G	C	0	.	DP=1	GT:GQ:DP	0/1:40:1	0|1:40:1
+1	100200	.	G	C	0	.	DP=1	GT:GQ:DP	0/0:40:1	0|1:40:1
+1	100300	.	G	C	0	.	DP=1	GT:GQ:DP	./.:40:1	1/1:40:1
+1	100400	.	C	G,T	35	.	DP=1	GT:GQ:DP	0/2:40:1	1/1:41:1
+1	100500	.	A	G	0	.	DP=1	GT:GQ:DP	0/0:40:1	1/1:40:1
+1	100600	.	C	G	0	.	DP=1	GT:GQ:DP	0/0:40:1	1/1:40:1

data/ext/vcftools/examples/.svn/text-base/subset.SNPs.out.svn-base

@@ -0,0 +1,10 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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">
+##FILTER=<ID=q10,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	100	.	G	C	1806	q10	DP=35	GT:GQ:DP	1/1:409:35
+1	120	.	T	G	628	q10	DP=21	GT:GQ:DP	0|1|1:21:21
+1	130	.	GAA	GTA	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22

data/ext/vcftools/examples/.svn/text-base/subset.indels.out.svn-base

@@ -0,0 +1,18 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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">
+##FILTER=<ID=q10,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	1/0:212:22
+1	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+1	150	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+1	160	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	100	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35
+2	110	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32
+2	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21
+2	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22
+2	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30
+2	150	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10
+2	160	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10

data/ext/vcftools/examples/.svn/text-base/subset.vcf.svn-base

@@ -0,0 +1,21 @@
+##fileformat=VCFv4.0
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##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">
+##FILTER=<ID=q10,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	100	.	G	C	1806	q10	DP=35	GT:GQ:DP	1/1:409:35	1/1:409:35
+1	110	.	C	.	1792	PASS	DP=32	GT:GQ:DP	0/0:245:32	0/0:245:32
+1	120	.	T	G	628	q10	DP=21	GT:GQ:DP	0|1|1:21:21	0|1|1:21:21
+1	130	.	GAA	G,GTA	1016	PASS	DP=22	GT:GQ:DP	1/2:212:22	1/2:212:22
+1	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30	0/1:150:30
+1	150	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10	1/2:12:10
+1	160	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10	1/2:12:10
+2	100	.	GTTT	G	1806	q10	DP=35	GT:GQ:DP	0/1:409:35	0/1:409:35
+2	110	.	CAAA	C	1792	PASS	DP=32	GT:GQ:DP	0/1:245:32	0/1:245:32
+2	120	.	GA	G	628	q10	DP=21	GT:GQ:DP	1/1:21:21	1/1:21:21
+2	130	.	GAA	G	1016	PASS	DP=22	GT:GQ:DP	0/1:212:22	0/1:212:22
+2	140	.	GT	G	727	PASS	DP=30	GT:GQ:DP	0/1:150:30	0/1:150:30
+2	150	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10	1/2:12:10
+2	160	.	TAAAA	TA,T	246	PASS	DP=10	GT:GQ:DP	1/2:12:10	1/2:12:10