From 18f62a346d6ba89583ab7aa2507e82b1db58937f Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 22 Jun 2010 18:38:03 +0000
Subject: [PATCH] fixing the tests; Bamboo captured the failure in the logs
 correctly.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3610 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../vcfWithGenotypes.vcf}                     |  3 ++-
 testdata/vcf/vcfWithoutGenotypes.vcf          | 20 +++++++++++++++++++
 2 files changed, 22 insertions(+), 1 deletion(-)
 rename testdata/{vcfExmaple.vcf4 => vcf/vcfWithGenotypes.vcf} (92%)
 create mode 100644 testdata/vcf/vcfWithoutGenotypes.vcf

diff --git a/testdata/vcfExmaple.vcf4 b/testdata/vcf/vcfWithGenotypes.vcf
similarity index 92%
rename from testdata/vcfExmaple.vcf4
rename to testdata/vcf/vcfWithGenotypes.vcf
index 9f9098a07..9bf4f4750 100644
--- a/testdata/vcfExmaple.vcf4
+++ b/testdata/vcf/vcfWithGenotypes.vcf
@@ -21,4 +21,5 @@
 20	1110696	rs6040355	A	G,T	67	PASS	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
 20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
 20	1234567	microsat1	GTCT	G,GTACT	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3
-20	1234587	supersite	GGGG	G	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/0:17:2	1/1:40:3
\ No newline at end of file
+20	1234587	supersite	GGGG	G	50	PASS	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/0:17:2	1/1:40:3
+22	17580633	.	ACNCCTAANCC	AC	100	PASS	NS=3;DP=9;AA=G	GT:GQ:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
\ No newline at end of file
diff --git a/testdata/vcf/vcfWithoutGenotypes.vcf b/testdata/vcf/vcfWithoutGenotypes.vcf
new file mode 100644
index 000000000..b8617aa6a
--- /dev/null
+++ b/testdata/vcf/vcfWithoutGenotypes.vcf
@@ -0,0 +1,20 @@
+##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=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">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2
+20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB
+20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ
+20	1234567	microsat1	GTCT	G,GTACT	50	PASS	NS=3;DP=9;AA=G
+20	1234587	supersite	GGGG	G	50	PASS	NS=3;DP=9;AA=G
\ No newline at end of file