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Adds a reader for NGS filter files and change some API for the apat library

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This commit is contained in:
Eric Coissac
2022-01-18 13:09:32 +01:00
parent 6571296bb2
commit 4551df08b1
13 changed files with 301 additions and 96 deletions
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20
pkg/obiformats/fastseq_obi_header.go
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@@ -173,16 +173,11 @@ func __is_false__(text []byte) bool {
bytes.Equal(text, __FALSE__)
}
func ParseFastSeqOBIHeader(sequence obiseq.BioSequence) {
definition := []byte(sequence.Definition())
annotations := sequence.Annotations()
// all_matches := __obi_header_pattern__.FindAllSubmatchIndex(definition, -1)
func ParseOBIFeatures(text string, annotations obiseq.Annotation) string {
definition := []byte(text)
d := definition
//for m := __obi_header_key_pattern__.FindIndex(definition); len(m) > 0; {
//fmt.Println(string(definition[0:20]), __match__key__(definition))
for m := __match__key__(definition); len(m) > 0; {
var bvalue []byte
var value interface{}
@@ -263,7 +258,16 @@ func ParseFastSeqOBIHeader(sequence obiseq.BioSequence) {
m = __match__key__(d)
}
sequence.SetDefinition(string(bytes.TrimSpace(d)))
return string(bytes.TrimSpace(d))
}
func ParseFastSeqOBIHeader(sequence obiseq.BioSequence) {
annotations := sequence.Annotations()
definition := ParseOBIFeatures(sequence.Definition(),
annotations)
sequence.SetDefinition(definition)
}
func FormatFastSeqOBIHeader(sequence obiseq.BioSequence) string {