obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

Big change iin the data model, and a first version of obiuniq

Browse Source
This commit is contained in:
Eric Coissac
2022-02-21 19:00:23 +01:00
parent 9737f97084
commit 2e7c1834b0
43 changed files with 664 additions and 440 deletions
Download Patch File Download Diff File Expand all files Collapse all files

12
pkg/obingslibrary/match.go
View File

@ -38,7 +38,7 @@ func (library *NGSLibrary) Compile(maxError int) error {
return nil
}
func (library *NGSLibrary) Match(sequence obiseq.BioSequence) *DemultiplexMatch {
func (library *NGSLibrary) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
for primers, marker := range *library {
m := marker.Match(sequence)
if m != nil {
@ -50,7 +50,7 @@ func (library *NGSLibrary) Match(sequence obiseq.BioSequence) *DemultiplexMatch
return nil
}
func (library *NGSLibrary) ExtractBarcode(sequence obiseq.BioSequence, inplace bool) (obiseq.BioSequence, error) {
func (library *NGSLibrary) ExtractBarcode(sequence *obiseq.BioSequence, inplace bool) (*obiseq.BioSequence, error) {
match := library.Match(sequence)
return match.ExtractBarcode(sequence, inplace)
}
@ -103,7 +103,7 @@ func (marker *Marker) Compile(forward, reverse string, maxError int) error {
return nil
}
func (marker *Marker) Match(sequence obiseq.BioSequence) *DemultiplexMatch {
func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
aseq, _ := obiapat.MakeApatSequence(sequence, false)
match := marker.forward.FindAllIndex(aseq, marker.taglength)
@ -134,7 +134,7 @@ func (marker *Marker) Match(sequence obiseq.BioSequence) *DemultiplexMatch {
srtag := ""
if err != nil {
rtag = obiseq.NilBioSequence
rtag = nil
} else {
rtag.ReverseComplement(true)
srtag = strings.ToLower(rtag.String())
@ -189,7 +189,7 @@ func (marker *Marker) Match(sequence obiseq.BioSequence) *DemultiplexMatch {
defer ftag.Recycle()
sftag := ""
if err != nil {
ftag = obiseq.NilBioSequence
ftag = nil
} else {
ftag = ftag.ReverseComplement(true)
@ -218,7 +218,7 @@ func (marker *Marker) Match(sequence obiseq.BioSequence) *DemultiplexMatch {
return nil
}
func (match *DemultiplexMatch) ExtractBarcode(sequence obiseq.BioSequence, inplace bool) (obiseq.BioSequence, error) {
func (match *DemultiplexMatch) ExtractBarcode(sequence *obiseq.BioSequence, inplace bool) (*obiseq.BioSequence, error) {
if !inplace {
sequence = sequence.Copy()
}