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[ngsfilter] Trim whitespace from primer and sample fields

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Trim leading/trailing whitespaces in forward/reverse primers, tags (via sample_tag), experiment andsample fields to prevent parsing errors due to formatting inconsistencies in input data.
This commit is contained in:
Eric Coissac
2026-04-30 08:14:10 +02:00
parent 42910c7db9
commit 14e2840a2d
1 changed files with 5 additions and 5 deletions
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pkg/obiformats/ngsfilter_read.go
+5 -5
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@@ -631,9 +631,9 @@ func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
return nil, fmt.Errorf("row %d has %d columns, expected %d", len(data), len(fields), len(header)) return nil, fmt.Errorf("row %d has %d columns, expected %d", len(data), len(fields), len(header))
} }
forward_primer := fields[forward_primerColIndex] forward_primer := strings.TrimSpace(fields[forward_primerColIndex])
reverse_primer := fields[reverse_primerColIndex] reverse_primer := strings.TrimSpace(fields[reverse_primerColIndex])
tags := _parseMainNGSFilterTags(fields[sample_tagColIndex]) tags := _parseMainNGSFilterTags(strings.TrimSpace(fields[sample_tagColIndex]))
marker, _ := ngsfilter.GetMarker(forward_primer, reverse_primer) marker, _ := ngsfilter.GetMarker(forward_primer, reverse_primer)
pcr, ok := marker.GetPCR(tags.Forward, tags.Reverse) pcr, ok := marker.GetPCR(tags.Forward, tags.Reverse)
@@ -644,8 +644,8 @@ func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
i, tags.Forward, tags.Reverse, forward_primer, reverse_primer) i, tags.Forward, tags.Reverse, forward_primer, reverse_primer)
} }
pcr.Experiment = fields[experimentColIndex] pcr.Experiment = strings.TrimSpace(fields[experimentColIndex])
pcr.Sample = fields[sampleColIndex] pcr.Sample = strings.TrimSpace(fields[sampleColIndex])
if extraColumns != nil { if extraColumns != nil {
pcr.Annotations = make(obiseq.Annotation) pcr.Annotations = make(obiseq.Annotation)