update modules and add tests for #150

go.mod

@@ -8,7 +8,7 @@ require (
 	github.com/brentp/bix v0.0.0-20190718140914-00aa7a7f205d
 	github.com/brentp/goluaez v0.0.0-20160116211227-dd35d08e32e7
 	github.com/brentp/irelate v0.0.1
-	github.com/brentp/vcfgo v0.0.0-20220919165057-adf3b5d20c55
+	github.com/brentp/vcfgo v0.0.0-20221128230736-759c0d32541e
 	github.com/brentp/xopen v0.0.0-20181116180855-111b45cadc7d
 	github.com/pkg/errors v0.9.1 // indirect
 	github.com/yuin/gluare v0.0.0-20170607022532-d7c94f1a80ed // indirect

tests/functional-test.sh

@@ -7,7 +7,10 @@ test -e ssshtest || wget -q https://raw.githubusercontent.com/ryanlayer/ssshtest
 set -o nounset
 
 
-go install -race -a github.com/brentp/vcfanno
+go build -race -a
+export PATH=.:$PATH
+echo using $(which vcfanno)
+
 
 run check_self_number vcfanno -base-path tests/data/ -lua example/custom.lua tests/data/number.conf tests/data/number-input.vcf
 assert_equal 0 $(grep -c "lua error in postannotation" $STDERR_FILE)
@@ -24,6 +27,10 @@ assert_equal 6 $(grep ^# $STDOUT_FILE | grep -c lua)
 # so lua_start doesn't exist.
 assert_equal 3 $(grep -c "not found in" $STDERR_FILE)
 
+run check_samples vcfanno -base-path tests/citest/ tests/citest/conf.toml  tests/citest/test.vcf
+n=$(grep -c ^#CHROM $STDOUT_FILE)
+assert_equal $n 1
+
 run check_ends vcfanno -ends -lua example/custom.lua example/conf.toml example/query.vcf.gz
 n=$(grep -v ^# $STDOUT_FILE | grep -c right_)
 assert_equal $(( $n > 0 )) 1