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Adds an error message when no sample can be associated

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This commit is contained in:
Eric Coissac
2022-02-18 09:58:56 +01:00
parent 2636882f9f
commit cb125bb2a4
1 changed files with 16 additions and 7 deletions
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19
pkg/obingslibrary/match.go
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@ -155,8 +155,7 @@ func (marker *Marker) Match(sequence obiseq.BioSequence) *DemultiplexMatch {
} }
err := fmt.Errorf("cannot locates reverse priming site") m.Error = fmt.Errorf("cannot locates reverse priming site")
m.Error = err
return &m return &m
} }
@ -211,8 +210,8 @@ func (marker *Marker) Match(sequence obiseq.BioSequence) *DemultiplexMatch {
return &m return &m
} }
err := fmt.Errorf("cannot locates forward priming site") m.Error = fmt.Errorf("cannot locates forward priming site")
m.Error = err
return &m return &m
} }
@ -232,11 +231,17 @@ func (match *DemultiplexMatch) ExtractBarcode(sequence obiseq.BioSequence, inpla
if match.ForwardMatch != "" && match.ReverseMatch != "" { if match.ForwardMatch != "" && match.ReverseMatch != "" {
var err error var err error
sequence, err = sequence.Subsequence(match.BarcodeStart, match.BarcodeEnd, false)
if match.BarcodeStart < match.BarcodeEnd {
sequence, err = sequence.Subsequence(match.BarcodeStart, match.BarcodeEnd, false)
if err != nil { if err != nil {
log.Fatalf("cannot extract sub sequence %d..%d %v", match.BarcodeStart, match.BarcodeEnd, *match) log.Fatalf("cannot extract sub sequence %d..%d %v", match.BarcodeStart, match.BarcodeEnd, *match)
} }
} else {
annot := sequence.Annotations()
annot["demultiplex_error"] = "read correponding to a primer dimer"
return sequence, errors.New("read correponding to a primer dimer")
}
} }
if !match.IsDirect { if !match.IsDirect {
@ -244,6 +249,7 @@ func (match *DemultiplexMatch) ExtractBarcode(sequence obiseq.BioSequence, inpla
} }
annot := sequence.Annotations() annot := sequence.Annotations()
if annot == nil { if annot == nil {
log.Fatalf("nil annot %v", sequence) log.Fatalf("nil annot %v", sequence)
} }
@ -278,6 +284,9 @@ func (match *DemultiplexMatch) ExtractBarcode(sequence obiseq.BioSequence, inpla
for k, val := range match.Pcr.Annotations { for k, val := range match.Pcr.Annotations {
annot[k] = val annot[k] = val
} }
} else {
annot["demultiplex_error"] = "cannot assign the sequence to a sample"
match.Error = errors.New("cannot assign the sequence to a sample")
} }
return sequence, match.Error return sequence, match.Error