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Patch the production of the ratio file

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This commit is contained in:
Eric Coissac
2025-02-27 10:19:39 +01:00
parent 791d253edc
commit 0067152c2b
6 changed files with 64 additions and 58 deletions
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24
pkg/obiformats/fastseq_json_header.go
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@ -13,7 +13,7 @@ import (
"github.com/buger/jsonparser"
)
func _parse_json_map_string(str []byte, sequence *obiseq.BioSequence) (map[string]string, error) {
func _parse_json_map_string(str []byte) (map[string]string, error) {
values := make(map[string]string)
jsonparser.ObjectEach(str,
func(key []byte, value []byte, dataType jsonparser.ValueType, offset int) (err error) {
@ -25,7 +25,7 @@ func _parse_json_map_string(str []byte, sequence *obiseq.BioSequence) (map[strin
return values, nil
}
func _parse_json_map_int(str []byte, sequence *obiseq.BioSequence) (map[string]int, error) {
func _parse_json_map_int(str []byte) (map[string]int, error) {
values := make(map[string]int)
jsonparser.ObjectEach(str,
func(key []byte, value []byte, dataType jsonparser.ValueType, offset int) (err error) {
@ -41,7 +41,7 @@ func _parse_json_map_int(str []byte, sequence *obiseq.BioSequence) (map[string]i
return values, nil
}
func _parse_json_map_float(str []byte, sequence *obiseq.BioSequence) (map[string]float64, error) {
func _parse_json_map_float(str []byte) (map[string]float64, error) {
values := make(map[string]float64)
jsonparser.ObjectEach(str,
func(key []byte, value []byte, dataType jsonparser.ValueType, offset int) (err error) {
@ -57,7 +57,7 @@ func _parse_json_map_float(str []byte, sequence *obiseq.BioSequence) (map[string
return values, nil
}
func _parse_json_map_bool(str []byte, sequence *obiseq.BioSequence) (map[string]bool, error) {
func _parse_json_map_bool(str []byte) (map[string]bool, error) {
values := make(map[string]bool)
jsonparser.ObjectEach(str,
func(key []byte, value []byte, dataType jsonparser.ValueType, offset int) (err error) {
@ -73,7 +73,7 @@ func _parse_json_map_bool(str []byte, sequence *obiseq.BioSequence) (map[string]
return values, nil
}
func _parse_json_map_interface(str []byte, sequence *obiseq.BioSequence) (map[string]interface{}, error) {
func _parse_json_map_interface(str []byte) (map[string]interface{}, error) {
values := make(map[string]interface{})
jsonparser.ObjectEach(str,
func(key []byte, value []byte, dataType jsonparser.ValueType, offset int) (err error) {
@ -100,7 +100,7 @@ func _parse_json_map_interface(str []byte, sequence *obiseq.BioSequence) (map[st
return values, nil
}
func _parse_json_array_string(str []byte, sequence *obiseq.BioSequence) ([]string, error) {
func _parse_json_array_string(str []byte) ([]string, error) {
values := make([]string, 0)
jsonparser.ArrayEach(str,
func(value []byte, dataType jsonparser.ValueType, offset int, err error) {
@ -162,7 +162,7 @@ func _parse_json_array_bool(str []byte, sequence *obiseq.BioSequence) ([]bool, e
return values, nil
}
func _parse_json_array_interface(str []byte, sequence *obiseq.BioSequence) ([]interface{}, error) {
func _parse_json_array_interface(str []byte) ([]interface{}, error) {
values := make([]interface{}, 0)
jsonparser.ArrayEach(str,
func(value []byte, dataType jsonparser.ValueType, offset int, err error) {
@ -261,14 +261,14 @@ func _parse_json_header_(header string, sequence *obiseq.BioSequence) string {
sequence.SetCount(int(count))
case skey == "obiclean_weight":
weight, err := _parse_json_map_int(value, sequence)
weight, err := _parse_json_map_int(value)
if err != nil {
log.Fatalf("%s: Cannot parse obiclean weight %s", sequence.Id(), string(value))
}
annotations[skey] = weight
case skey == "obiclean_status":
status, err := _parse_json_map_string(value, sequence)
status, err := _parse_json_map_string(value)
if err != nil {
log.Fatalf("%s: Cannot parse obiclean status %s", sequence.Id(), string(value))
}
@ -276,7 +276,7 @@ func _parse_json_header_(header string, sequence *obiseq.BioSequence) string {
case strings.HasPrefix(skey, "merged_"):
if dataType == jsonparser.Object {
data, err := _parse_json_map_int(value, sequence)
data, err := _parse_json_map_int(value)
if err != nil {
log.Fatalf("%s: Cannot parse merged slot %s: %v", sequence.Id(), skey, err)
} else {
@ -316,9 +316,9 @@ func _parse_json_header_(header string, sequence *obiseq.BioSequence) string {
annotations[skey], err = strconv.ParseFloat(obiutils.UnsafeString(value), 64)
}
case jsonparser.Array:
annotations[skey], err = _parse_json_array_interface(value, sequence)
annotations[skey], err = _parse_json_array_interface(value)
case jsonparser.Object:
annotations[skey], err = _parse_json_map_interface(value, sequence)
annotations[skey], err = _parse_json_map_interface(value)
case jsonparser.Boolean:
annotations[skey], err = jsonparser.ParseBoolean(value)
case jsonparser.Null: