Add test for #2526

Author: pd3

test/annotate.pipes.1.out

@@ -0,0 +1,9 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=1>
+##INFO=<ID=SRC,Number=.,Type=String,Description="">
+##INFO=<ID=II,Number=1,Type=Integer,Description="">
+##INFO=<ID=FF,Number=1,Type=Float,Description="">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	123456	.	C	CT	.	.	SRC=chr5|123456|C|A,CT,G|2;FF=1.1;II=111
+1	123456	.	C	CT	.	.	SRC=chr5|123456|C|A,CT,G|2;FF=1.1;II=111

test/annotate.pipes.2.out

@@ -0,0 +1,9 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=1>
+##INFO=<ID=SRC,Number=.,Type=String,Description="">
+##INFO=<ID=II,Number=1,Type=Integer,Description="">
+##INFO=<ID=FF,Number=1,Type=Float,Description="">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	123456	.	C	CT	.	.	SRC=chr5|123456|C|A,CT,G|2;FF=1.1;II=111
+1	123456	.	C	CT	.	.	SRC=chr5|123457|TA|AA,CA,TGA|3;FF=2.2;II=222

test/annotate.pipes.tab

@@ -0,0 +1,2 @@
+1	123456	C	CT	chr5|123456|C|A,CT,G|2	1.1	111
+1	123456	C	CT	chr5|123457|TA|AA,CA,TGA|3	2.2	222

test/annotate.pipes.vcf

@@ -0,0 +1,8 @@
+##fileformat=VCFv4.2
+##contig=<ID=1>
+##INFO=<ID=SRC,Number=.,Type=String,Description="">
+##INFO=<ID=II,Number=1,Type=Integer,Description="">
+##INFO=<ID=FF,Number=1,Type=Float,Description="">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	123456	.	C	CT	.	.	SRC=chr5|123456|C|A,CT,G|2
+1	123456	.	C	CT	.	.	SRC=chr5|123457|TA|AA,CA,TGA|3

test/test.pl

@@ -565,6 +565,8 @@
 run_test(\&test_vcf_sort,$opts,in=>'sort',out=>'sort.out',args=>q[-m 0],fmt=>'%CHROM\\t%POS\\t%REF,%ALT\\n');
 run_test(\&test_vcf_sort,$opts,in=>'sort',out=>'sort.out',args=>q[-m 1000],fmt=>'%CHROM\\t%POS\\t%REF,%ALT\\n');
 run_test(\&test_vcf_regions,$opts,in=>'regions');
+run_test(\&test_vcf_annotate,$opts,in=>'annotate.pipes',tab=>'annotate.pipes',out=>'annotate.pipes.1.out',args=>q[-c CHROM,POS,REF,ALT,SRC,FF,II]);
+run_test(\&test_vcf_annotate,$opts,in=>'annotate.pipes',tab=>'annotate.pipes',out=>'annotate.pipes.2.out',args=>q[-c CHROM,POS,REF,ALT,SRC,FF,II -k -i 'SRC={SRC}']);
 run_test(\&test_vcf_annotate,$opts,in=>'annotate.AR',tab=>'annotate.AR',out=>'annotate.AR.1.out',args=>q[-c CHROM,POS,REF,ALT,+INFO/IA,+INFO/FA,+INFO/IR,+INFO/FR]);
 run_test(\&test_vcf_annotate,$opts,in=>'annotate.AR',tab=>'annotate.AR',out=>'annotate.AR.2.out',args=>q[-c CHROM,POS,REF,ALT,INFO/IA,INFO/FA,INFO/IR,INFO/FR]);
 run_test(\&test_vcf_annotate,$opts,in=>'annotate.int.dst',vcf=>'annotate.int.src',out=>'annotate.int.1.out',args=>q[-c +INFO/IA,+INFO/IR]);