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Patch sequence writers to remove definition from header when json format is used.

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Former-commit-id: a8a74cccb52d577d4ea1c0ad88b121a8e511149d
This commit is contained in:
Eric Coissac
2023-10-05 07:31:31 +02:00
parent d23a911080
commit 0a8f7afb2a
5 changed files with 27 additions and 27 deletions
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36
pkg/obiformats/fastseq_obi_header.go
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@ -298,27 +298,29 @@ func FormatFastSeqOBIHeader(sequence *obiseq.BioSequence) string {
var text strings.Builder
for key, value := range annotations {
switch t := value.(type) {
case string:
text.WriteString(fmt.Sprintf("%s=%s; ", key, t))
case map[string]int,
map[string]string,
map[string]interface{},
obiseq.StatsOnValues:
tv, err := obiutils.JsonMarshal(t)
if err != nil {
log.Fatalf("Cannot convert %v value", value)
if key != "definition" {
switch t := value.(type) {
case string:
text.WriteString(fmt.Sprintf("%s=%s; ", key, t))
case map[string]int,
map[string]string,
map[string]interface{},
obiseq.StatsOnValues:
tv, err := obiutils.JsonMarshal(t)
if err != nil {
log.Fatalf("Cannot convert %v value", value)
}
tv = bytes.ReplaceAll(tv, []byte(`"`), []byte("'"))
text.WriteString(fmt.Sprintf("%s=", key))
text.Write(tv)
text.WriteString("; ")
default:
text.WriteString(fmt.Sprintf("%s=%v; ", key, value))
}
tv = bytes.ReplaceAll(tv, []byte(`"`), []byte("'"))
text.WriteString(fmt.Sprintf("%s=", key))
text.Write(tv)
text.WriteString("; ")
default:
text.WriteString(fmt.Sprintf("%s=%v; ", key, value))
}
}
return text.String()
return text.String() + " " + sequence.Definition()
}
return ""