From 034e5496dcd7c51f548b5d375bfb22641af50c28 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 13 Nov 2023 14:55:10 +0100
Subject: [PATCH] small race condition fix

---
 convert/structs.go  | 21 +++++++++++----------
 convert/vcf.go      | 21 +++++++++++----------
 convert/vcf_test.go | 26 ++++++++++++++++----------
 3 files changed, 38 insertions(+), 30 deletions(-)

diff --git a/convert/structs.go b/convert/structs.go
index 97aadfc..ea7f116 100644
--- a/convert/structs.go
+++ b/convert/structs.go
@@ -74,22 +74,23 @@ type HeaderLine struct {
 
 // The struct for one variant
 type Variant struct {
-	Chrom  string               // The chromosome
-	Pos    string               // The position
-	Id     string               // The ID
-	Ref    string               // The reference allele
-	Alt    string               // The alternative allele
-	Qual   string               // The quality
-	Filter string               // The filter
-	Info   MapVariantInfoFormat // The info fields
-	Format MapVariantInfoFormat // The format fields
+	Chrom  string                 // The chromosome
+	Pos    string                 // The position
+	Id     string                 // The ID
+	Ref    string                 // The reference allele
+	Alt    string                 // The alternative allele
+	Qual   string                 // The quality
+	Filter string                 // The filter
+	Info   SliceVariantInfoFormat // The info fields
+	Format SliceVariantInfoFormat // The format fields
 }
 
 // The map for the info and format fields
-type MapVariantInfoFormat map[string]VariantInfoFormat
+type SliceVariantInfoFormat []VariantInfoFormat
 
 // The struct for one info or format field
 type VariantInfoFormat struct {
+	Name   string // The name of the current INFO or FORMAT field
 	Number string // The number of values that can be included in the INFO field (e.g. 1, 2, A, R)
 	Type   string // The type of the header field (e.g. Integer, Float, Character, Flag)
 	Value  string // The value of the field
diff --git a/convert/vcf.go b/convert/vcf.go
index 177f375..ad945af 100644
--- a/convert/vcf.go
+++ b/convert/vcf.go
@@ -218,18 +218,19 @@ func (v *Vcf) AddVariants(cCtx *cli.Context, config Config) error {
 }
 
 // Get the values of all info fields and transform them to a map
-func (mcifs *SliceConfigInfoFormatStruct) getValues(values []string, header []string) (error, MapVariantInfoFormat) {
-	infoMap := MapVariantInfoFormat{}
+func (mcifs *SliceConfigInfoFormatStruct) getValues(values []string, header []string) (error, SliceVariantInfoFormat) {
+	infoMap := SliceVariantInfoFormat{}
 	for _, v := range *mcifs {
 		err, value := v.getValue(values, header)
 		if err != nil {
 			return err, nil
 		}
-		infoMap[v.Name] = VariantInfoFormat{
+		infoMap = append(infoMap, VariantInfoFormat{
+			Name:   v.Name,
 			Number: v.Number,
 			Type:   v.Type,
 			Value:  value,
-		}
+		})
 	}
 	return nil, infoMap
 }
@@ -312,10 +313,10 @@ func (v Variant) String(count int) string {
 }
 
 // Convert the info map to a string
-func (mvif MapVariantInfoFormat) infoString() string {
+func (mvif SliceVariantInfoFormat) infoString() string {
 	var infoSlice []string
-	for k, v := range mvif {
-		upperInfo := strings.ToUpper(k)
+	for _, v := range mvif {
+		upperInfo := strings.ToUpper(v.Name)
 		switch infoType := strings.ToLower(v.Type); infoType {
 		case "flag":
 			infoSlice = append(infoSlice, upperInfo)
@@ -328,11 +329,11 @@ func (mvif MapVariantInfoFormat) infoString() string {
 }
 
 // Convert the format map to a string
-func (mcifs MapVariantInfoFormat) formatString() string {
+func (mvif SliceVariantInfoFormat) formatString() string {
 	var formatField []string
 	var formatValues []string
-	for k, v := range mcifs {
-		upperFormat := strings.ToUpper(k)
+	for _, v := range mvif {
+		upperFormat := strings.ToUpper(v.Name)
 		formatField = append(formatField, upperFormat)
 		formatValues = append(formatValues, v.Value)
 	}
diff --git a/convert/vcf_test.go b/convert/vcf_test.go
index f585eff..9b34825 100644
--- a/convert/vcf_test.go
+++ b/convert/vcf_test.go
@@ -213,15 +213,17 @@ func TestVariantString(t *testing.T) {
 		Alt:    "C",
 		Qual:   "100",
 		Filter: "PASS",
-		Info: MapVariantInfoFormat{
-			"SVLEN": VariantInfoFormat{
+		Info: SliceVariantInfoFormat{
+			{
+				Name:   "SVLEN",
 				Number: "1",
 				Type:   "Integer",
 				Value:  "100",
 			},
 		},
-		Format: MapVariantInfoFormat{
-			"GT": VariantInfoFormat{
+		Format: SliceVariantInfoFormat{
+			{
+				Name:   "GT",
 				Number: "1",
 				Type:   "String",
 				Value:  "0/1",
@@ -241,25 +243,29 @@ func TestVariantString(t *testing.T) {
 		Alt:    "C",
 		Qual:   "100",
 		Filter: "PASS",
-		Info: MapVariantInfoFormat{
-			"SVLEN": VariantInfoFormat{
+		Info: SliceVariantInfoFormat{
+			{
+				Name:   "SVLEN",
 				Number: "1",
 				Type:   "Integer",
 				Value:  "100",
 			},
-			"SVTYPE": VariantInfoFormat{
+			{
+				Name:   "SVTYPE",
 				Number: "1",
 				Type:   "String",
 				Value:  "DEL",
 			},
 		},
-		Format: MapVariantInfoFormat{
-			"GT": VariantInfoFormat{
+		Format: SliceVariantInfoFormat{
+			{
+				Name:   "GT",
 				Number: "1",
 				Type:   "String",
 				Value:  "0/1",
 			},
-			"CN": VariantInfoFormat{
+			{
+				Name:   "CN",
 				Number: "1",
 				Type:   "Integer",
 				Value:  "2",