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Change the way sequence definition are managed. They are now when present stored as an attribute

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Former-commit-id: 6e618377c05b42937d2eace3c9668390980ab68c
This commit is contained in:
Eric Coissac
2023-10-05 07:21:12 +02:00
parent 5c30ec354f
commit d23a911080
11 changed files with 115 additions and 30 deletions
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19
pkg/obingslibrary/match.go
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@ -104,6 +104,16 @@ func (marker *Marker) Compile(forward, reverse string, maxError int, allowsIndel
return nil
}
// Match finds the best matching demultiplex for a given sequence.
//
// Parameters:
//
// marker - a pointer to a Marker struct that contains the forward and reverse primers.
// sequence - a pointer to a BioSequence struct that represents the input sequence.
//
// Returns:
//
// A pointer to a DemultiplexMatch struct that contains the best matching demultiplex.
func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
aseq, _ := obiapat.MakeApatSequence(sequence, false)
@ -223,6 +233,15 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
return nil
}
// ExtractBarcode extracts the barcode from the given biosequence.
//
// Parameters:
// - sequence: The biosequence from which to extract the barcode.
// - inplace: A boolean indicating whether the barcode should be extracted in-place or not.
//
// Returns:
// - The biosequence with the extracted barcode.
// - An error indicating any issues encountered during the extraction process.
func (match *DemultiplexMatch) ExtractBarcode(sequence *obiseq.BioSequence, inplace bool) (*obiseq.BioSequence, error) {
if !inplace {
sequence = sequence.Copy()