In obimultiplex, patch a bug when no tag are associated to a primer.

pkg/obiformats/ngsfilter_read.go

@@ -536,6 +536,24 @@ var library_parameter = map[string]func(library *obingslibrary.NGSLibrary, value
 	},
 }
 
+// ReadCSVNGSFilter reads an NGS filter configuration from a CSV file and returns
+// an NGSLibrary. The CSV file must include columns for 'experiment', 'sample',
+// 'sample_tag', 'forward_primer', and 'reverse_primer'. Additional columns are
+// used to annotate PCR samples.
+//
+// Parameters:
+//   - reader: an io.Reader providing the CSV input.
+//
+// Returns:
+//   - A pointer to an NGSLibrary populated with the data from the CSV file.
+//   - An error if the CSV is malformed or required columns are missing.
+//
+// The function processes both data records and parameter lines starting with
+// '@param'. Parameter lines configure various aspects of the library.
+//
+// Each row in the CSV is validated to ensure it has the correct number of columns.
+// Duplicate tag pairs for the same marker result in an error. Primer unicity is
+// checked, and any unknown parameters are logged as warnings.
 func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
 	ngsfilter := obingslibrary.MakeNGSLibrary()
 	file := csv.NewReader(reader)
@@ -576,6 +594,7 @@ func ReadCSVNGSFilter(reader io.Reader) (*obingslibrary.NGSLibrary, error) {
 	extraColumns := make([]int, 0)
 
 	for i, colName := range header {
+
 		switch colName {
 		case "experiment":
 			experimentColIndex = i

pkg/obingslibrary/multimatch.go

@@ -343,6 +343,10 @@ func (marker *Marker) beginTagExtractor(
 	// log.Warnf("Forward : %v -> %d %c", forward, marker.Forward_spacer, marker.Forward_tag_delimiter)
 	// log.Warnf("Forward : %v -> %d %c", forward, marker.Reverse_spacer, marker.Reverse_tag_delimiter)
 	if forward {
+		if marker.Forward_tag_length == 0 {
+			return ""
+		}
+
 		if marker.Forward_tag_delimiter == 0 {
 			return marker.beginFixedTagExtractor(sequence, begin, forward)
 		} else {
@@ -355,6 +359,10 @@ func (marker *Marker) beginTagExtractor(
 			}
 		}
 	} else {
+		if marker.Reverse_tag_length == 0 {
+			return ""
+		}
+
 		if marker.Reverse_tag_delimiter == 0 {
 			return marker.beginFixedTagExtractor(sequence, begin, forward)
 		} else {
@@ -374,6 +382,10 @@ func (marker *Marker) endTagExtractor(
 	end int,
 	forward bool) string {
 	if forward {
+		if marker.Reverse_tag_length == 0 {
+			return ""
+		}
+
 		if marker.Reverse_tag_delimiter == 0 {
 			return marker.endFixedTagExtractor(sequence, end, forward)
 		} else {
@@ -386,6 +398,10 @@ func (marker *Marker) endTagExtractor(
 			}
 		}
 	} else {
+		if marker.Forward_tag_length == 0 {
+			return ""
+		}
+
 		if marker.Forward_tag_delimiter == 0 {
 			return marker.endFixedTagExtractor(sequence, end, forward)
 		} else {

pkg/obioptions/version.go

@@ -7,7 +7,7 @@ import (
 // TODO: The version number is extracted from git. This induces that the version
 // corresponds to the last commit, and not the one when the file will be
 // commited
-var _Commit = "74280e4"
+var _Commit = "9e8a7fd"
 var _Version = "Release 4.2.0"
 
 // Version returns the version of the obitools package.