Add defaults

CHANGELOG.md

@@ -1,3 +1,6 @@
+# 0.2.0dev
+- Added the `defaults` type to the `info` and `format` configuration. Defaults for resolvable fields can be set this way.
+
 # 0.1.2 - Adjust
 ## Fixes
 - Fixed a bug where the output VCF has no header when the input VCF has no variants

docs/configuration.md

@@ -41,6 +41,9 @@ info:
 ### value
 The `value` field can be used to change the default value of the info field. The value can be resolved (see [Resolvable fields](#resolvable-fields)).
 
+### defaults
+The `defaults` field can be used to define defaults for resolvable `INFO` and `FORMAT` fields. These defaults will be used when the required field is missing from the variant. 
+
 ### type
 The `type` field can be used to set the type of the info field (This will be reflected in the header of the output VCF file).
 
@@ -58,6 +61,8 @@ For example when all `SVLEN` info fields are positive, you maybe want to change
 info:
   SVLEN:
     value: $INFO/SVLEN
+    defaults:
+      $INFO/SVLEN: "-1"
     type: Integer
     description: "Structural variant length"
     number: 1
@@ -71,6 +76,9 @@ The `format` section can be used to change the format fields for each variant. T
 format:
   <format_field>:
     value: <new_value>
+    defaults:
+      <resolvable-field>: <default>
+      <resolvable-field>: <default>
     type: <new_type>
     description: <new_description>
     number: <new_number>

svync_api/config.go

@@ -79,7 +79,10 @@ func (config *Config) defineMissing() {
 	// Format fields
 	if _, ok := config.Format["GT"]; !ok {
 		config.Format["GT"] = ConfigInput{
-			Value:       "$FORMAT/GT",
+			Value: "$FORMAT/GT",
+			Defaults: map[string]string{
+				"$FORMAT/GT": "./.",
+			},
 			Number:      "1",
 			Type:        "String",
 			Description: "Genotype",

svync_api/execute.go

@@ -20,10 +20,10 @@ func Execute(Cctx *cli.Context, config *Config) {
 
 	file := Cctx.String("input")
 	inputVcf, err := os.Open(file)
-	defer inputVcf.Close()
 	if err != nil {
 		logger.Fatal(err)
 	}
+	defer inputVcf.Close()
 	header := newHeader()
 	breakEndVariants := &map[string]Variant{}
 	headerIsMade := false

svync_api/resolve.go

@@ -12,7 +12,7 @@ import (
 )
 
 // Resolve a value
-func ResolveValue(input string, variant *Variant, format *VariantFormat, Cctx *cli.Context) string {
+func ResolveValue(input string, variant *Variant, format *VariantFormat, Cctx *cli.Context, config *Config) string {
 	logger := log.New(os.Stderr, "", 0)
 
 	// Replace all the FORMAT fields
@@ -21,16 +21,19 @@ func ResolveValue(input string, variant *Variant, format *VariantFormat, Cctx *c
 	if len(allFormats) > 0 && format == nil {
 		logger.Fatalf("Cannot use a FORMAT field in a non-FORMAT context, please check your config file")
 	}
-	for _, stringToReplace := range allFormats {
-		fieldSlice := strings.Split(stringToReplace, "/")
+	for _, rawField := range allFormats {
+		fieldSlice := strings.Split(rawField, "/")
 
 		field := fieldSlice[1]
 		formatValue, ok := format.Content[field]
 
-		// TODO implement some alternative way to handle missing fields
 		if !ok {
-			if !Cctx.Bool("mute-warnings") {
-				logger.Printf("The field %s is not present in the FORMAT fields of the variant with ID %s, excluding it from this variant", field, variant.Id)
+			// Check if the field is a default value
+			defaults := config.Format[field].Defaults
+			if defaultValue, ok := defaults[rawField]; ok {
+				formatValue = []string{defaultValue}
+			} else if !Cctx.Bool("mute-warnings") {
+				logger.Printf("The field %s is not present in the FORMAT fields of the variant with ID %s, excluding it from this variant. Supply a default to mute this warning", field, variant.Id)
 			}
 		} else if len(fieldSlice) > 2 {
 			index, err := strconv.ParseInt(fieldSlice[2], 0, 64)
@@ -39,23 +42,26 @@ func ResolveValue(input string, variant *Variant, format *VariantFormat, Cctx *c
 			}
 			formatValue = []string{formatValue[index]}
 		}
-		input = strings.ReplaceAll(input, stringToReplace, strings.Join(formatValue, ","))
+		input = strings.ReplaceAll(input, rawField, strings.Join(formatValue, ","))
 	}
 
 	// Replace all the INFO fields
 	infoRegex := regexp.MustCompile(`\$INFO/[\w\d]+(/\d+)?`)
 	allInfos := infoRegex.FindAllString(input, -1)
-	for _, stringToReplace := range allInfos {
-		fieldSlice := strings.Split(stringToReplace, "/")
+	for _, rawField := range allInfos {
+		fieldSlice := strings.Split(rawField, "/")
 
 		field := fieldSlice[1]
 		info, ok := variant.Info[field]
 
-		// TODO implement some alternative way to handle missing fields
 		if !ok {
+			// Check if the field is a default value
+			defaults := config.Info[field].Defaults
 			infoType := variant.Header.Info[field].Type
-			if infoType != "Flag" && !Cctx.Bool("mute-warnings") {
-				logger.Printf("The field %s is not present in the INFO fields of the variant with ID %s, excluding it from this variant", field, variant.Id)
+			if defaultValue, ok := defaults[rawField]; ok {
+				info = []string{defaultValue}
+			} else if infoType != "Flag" && !Cctx.Bool("mute-warnings") {
+				logger.Printf("The field %s is not present in the FORMAT fields of the variant with ID %s, excluding it from this variant. Supply a default to mute this warning", field, variant.Id)
 			}
 		} else if len(fieldSlice) > 2 {
 			index, err := strconv.ParseInt(fieldSlice[2], 0, 64)
@@ -64,7 +70,7 @@ func ResolveValue(input string, variant *Variant, format *VariantFormat, Cctx *c
 			}
 			info = []string{info[index]}
 		}
-		input = strings.ReplaceAll(input, stringToReplace, strings.Join(info, ","))
+		input = strings.ReplaceAll(input, rawField, strings.Join(info, ","))
 	}
 
 	// Replace POS fields

svync_api/standardize.go

@@ -102,7 +102,7 @@ func (variant *Variant) standardize(config *Config, Cctx *cli.Context, count int
 		}
 	}
 
-	standardizedVariant.Id = fmt.Sprintf("%s_%v", ResolveValue(config.Id, variant, nil, Cctx), count)
+	standardizedVariant.Id = fmt.Sprintf("%s_%v", ResolveValue(config.Id, variant, nil, Cctx, config), count)
 
 	// Add info fields
 	for name, infoConfig := range config.Info {
@@ -114,7 +114,7 @@ func (variant *Variant) standardize(config *Config, Cctx *cli.Context, count int
 		if value == "" {
 			continue
 		}
-		standardizedVariant.Info[name] = []string{ResolveValue(value, variant, nil, Cctx)}
+		standardizedVariant.Info[name] = []string{ResolveValue(value, variant, nil, Cctx, config)}
 	}
 
 	// Add format fields
@@ -127,7 +127,7 @@ func (variant *Variant) standardize(config *Config, Cctx *cli.Context, count int
 			if val, ok := formatConfig.Alts[sVType]; ok {
 				value = val
 			}
-			newFormat.Content[name] = []string{ResolveValue(value, variant, &format, Cctx)}
+			newFormat.Content[name] = []string{ResolveValue(value, variant, &format, Cctx, config)}
 		}
 		standardizedVariant.Format[sample] = *newFormat
 	}

svync_api/structs.go

@@ -62,6 +62,7 @@ type Config struct {
 type MapConfigInput map[string]ConfigInput
 type ConfigInput struct {
 	Value       string
+	Defaults    map[string]string
 	Description string
 	Number      string
 	Type        string

svync_api/variant.go

@@ -45,10 +45,10 @@ func toBreakPoint(mate1 *Variant, mate2 *Variant) *Variant {
 		filter = mate1.Filter
 	}
 
-	varQual, err := strconv.ParseFloat(mate1.Qual, 64)
-	mateQual, err := strconv.ParseFloat(mate2.Qual, 64)
+	varQual, err1 := strconv.ParseFloat(mate1.Qual, 64)
+	mateQual, err2 := strconv.ParseFloat(mate2.Qual, 64)
 	qual := "."
-	if err == nil {
+	if err1 == nil && err2 == nil {
 		qual = fmt.Sprintf("%f", (varQual+mateQual)/2)
 	}