handle by_alt + float correctly

closes #113

api/api.go

@@ -540,6 +540,13 @@ func (s *Source) UpdateHeader(r HeaderUpdater, ends bool, htype string, number s
 	if s.Op == "by_alt" {
 		number = "A"
 		ntype = "String"
+		if strings.HasSuffix(s.Name, "_float") {
+			ntype = "Float"
+			s.Name = s.Name[:len(s.Name)-6]
+		} else if strings.HasSuffix(s.Name, "_int") {
+			ntype = "Integer"
+			s.Name = s.Name[:len(s.Name)-4]
+		}
 		// for 'self' and 'first', we can get the type from the header of the annotation file.
 	} else if htype != "" && (s.Op == "self" || s.Op == "first") {
 		ntype = htype

tests/by_alt_float/conf.toml

@@ -0,0 +1,5 @@
+[[annotation]]
+names = ["CADD_RAW_float"]
+file = "annotation.tsv.gz"
+columns = [5]
+ops = ["by_alt"]

tests/by_alt_float/q.vcf

@@ -0,0 +1,7 @@
+##fileformat=VCFv4.2
+##contig=<ID=chr2,length=242193529,assembly=GRCh38>
+##INFO=<ID=AF,Number=.,Type=Float,Description="">
+##INFO=<ID=AQ,Number=.,Type=Integer,Description="">
+##hailversion=0.2.9-8588a25687af
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+chr2	41647	2_41647_A_G	A	G	1328.0	.	AF=1.56250e-02;AQ=1328

tests/functional-test.sh

@@ -187,3 +187,10 @@ run self_test_with_A_and_many_overlaps fn_self_test_with_A_and_many_overlaps
 assert_exit_code 0
 assert_equal $(tail -1 $STDOUT_FILE | cut -f 8) "AC=35,65;GN_AF=0.3717,0.6122"
 assert_in_stdout "ID=GN_AF,Number=A"
+
+
+run check_by_alts_float vcfanno -base-path tests/by_alt_float/ tests/by_alt_float/conf.toml tests/by_alt_float/q.vcf
+assert_exit_code 0
+assert_equal $(tail -1 $STDOUT_FILE | cut -f 8) "AF=1.56250e-02;AQ=1328;CADD_RAW=0.591814"
+go install -a
+