From 14e2840a2df289bde07439e5adbe89ec3ebf5d00 Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Thu, 30 Apr 2026 08:14:10 +0200 Subject: [PATCH] [ngsfilter] Trim whitespace from primer and sample fields 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. --- pkg/obiformats/ngsfilter_read.go | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/pkg/obiformats/ngsfilter_read.go b/pkg/obiformats/ngsfilter_read.go index 57075c0..1755fda 100644 --- a/pkg/obiformats/ngsfilter_read.go +++ b/pkg/obiformats/ngsfilter_read.go @@ -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)) } - forward_primer := fields[forward_primerColIndex] - reverse_primer := fields[reverse_primerColIndex] - tags := _parseMainNGSFilterTags(fields[sample_tagColIndex]) + forward_primer := strings.TrimSpace(fields[forward_primerColIndex]) + reverse_primer := strings.TrimSpace(fields[reverse_primerColIndex]) + tags := _parseMainNGSFilterTags(strings.TrimSpace(fields[sample_tagColIndex])) marker, _ := ngsfilter.GetMarker(forward_primer, reverse_primer) 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) } - pcr.Experiment = fields[experimentColIndex] - pcr.Sample = fields[sampleColIndex] + pcr.Experiment = strings.TrimSpace(fields[experimentColIndex]) + pcr.Sample = strings.TrimSpace(fields[sampleColIndex]) if extraColumns != nil { pcr.Annotations = make(obiseq.Annotation)