From 9724fbbe0a91ca1b17ded3ec8c801707fef0e8f1 Mon Sep 17 00:00:00 2001
From: Neil Kindlon <nek3d@d-128-109-67.bootp.Virginia.EDU>
Date: Wed, 27 May 2015 16:20:06 -0400
Subject: [PATCH] Added extra unit test for vcf svlen - single # at end of line

---
 test/intersect/bug223_f.vcf      |  3 +++
 test/intersect/test-intersect.sh | 14 ++++++++++++++
 2 files changed, 17 insertions(+)
 create mode 100644 test/intersect/bug223_f.vcf

diff --git a/test/intersect/bug223_f.vcf b/test/intersect/bug223_f.vcf
new file mode 100644
index 00000000..ba983036
--- /dev/null
+++ b/test/intersect/bug223_f.vcf
@@ -0,0 +1,3 @@
+##fileformat=VCFv4.1
+chr1	1	a	G	<DEL>	70.90	.	TOOL=LUMPY;SVTYPE=DEL;SVLEN=-389,-4611;END=253195;STR=+-:4;IMPRECISE;CIPOS=-2,137;CIEND=0,0;EVENT=791255;SUP=4;PESUP=4;SRSUP=0;EV=PE;PRIN;CSQ=intergenic_variant||||||||||
+chr1	4	a	G	<DEL>	70.90	.	TOOL=LUMPY;SVTYPE=DEL;END=253195;STR=+-:4;IMPRECISE;CIPOS=-2,137;CIEND=0,0;EVENT=791255;SUP=4;PESUP=4;SRSUP=0;EV=PE;PRIN;CSQ=intergenic_variant||||||||||;SVLEN=-10
\ No newline at end of file
diff --git a/test/intersect/test-intersect.sh b/test/intersect/test-intersect.sh
index 76e211ec..7e8cc32d 100644
--- a/test/intersect/test-intersect.sh
+++ b/test/intersect/test-intersect.sh
@@ -610,6 +610,20 @@ $BT intersect -a bug223_e.vcf -b bug223_e.vcf | cut -f1-6 > obs
 check exp obs
 rm exp obs
 
+##################################################################
+# see that SVLEN in VCF files can handle single numbers,
+# at end of line, followed by null
+##################################################################
+echo "    intersect.t50...\c"
+echo \
+"chr1	1	a	G	<DEL>	70.90
+chr1	1	a	G	<DEL>	70.90
+chr1	4	a	G	<DEL>	70.90
+chr1	4	a	G	<DEL>	70.90" > exp
+$BT intersect -a bug223_f.vcf -b bug223_f.vcf | cut -f1-6 > obs
+check exp obs
+rm exp obs
+
 
 
 cd multi_intersect
-- 
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