Adds the command obimultiplex

pkg/obiformats/ngsfilter_read.go

@@ -6,29 +6,10 @@ import (
 	"io"
 	"strings"
 
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obingslibrary"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )
 
-type PrimerPair struct {
-	Forward string
-	Reverse string
-}
-
-type TagPair struct {
-	Forward string
-	Reverse string
-}
-
-type PCR struct {
-	Experiment  string
-	Sample      string
-	Partial     bool
-	Annotations obiseq.Annotation
-}
-
-type PCRs map[TagPair]PCR
-type NGSFilter map[PrimerPair]PCRs
-
 func _readLines(reader io.Reader) []string {
 	r := bufio.NewReader(reader)
 	bytes := []byte{}
@@ -53,12 +34,15 @@ func _readLines(reader io.Reader) []string {
 	return lines
 }
 
-func _parseMainNGSFilterTags(text string) TagPair {
+func _parseMainNGSFilterTags(text string) obingslibrary.TagPair {
 
 	tags := strings.Split(text, ":")
 
 	if len(tags) == 1 {
-		return TagPair{tags[0], tags[0]}
+		return obingslibrary.TagPair{
+			Forward: tags[0],
+			Reverse: tags[0],
+		}
 	}
 
 	if tags[0] == "-" {
@@ -69,28 +53,34 @@ func _parseMainNGSFilterTags(text string) TagPair {
 		tags[1] = ""
 	}
 
-	return TagPair{tags[0], tags[1]}
+	return obingslibrary.TagPair{
+		Forward: tags[0],
+		Reverse: tags[1],
+	}
 }
 
-func _parseMainNGSFilter(text string) (PrimerPair, TagPair, string, string, bool) {
+func _parseMainNGSFilter(text string) (obingslibrary.PrimerPair, obingslibrary.TagPair, string, string, bool) {
 	fields := strings.Fields(text)
 
 	tags := _parseMainNGSFilterTags(fields[2])
 	partial := fields[5] == "T" || fields[5] == "t"
 
-	return PrimerPair{fields[3], fields[4]},
+	return obingslibrary.PrimerPair{
+			Forward: fields[3],
+			Reverse: fields[4],
+		},
 		tags,
 		fields[0],
 		fields[1],
 		partial
 }
 
-func ReadNGSFilter(reader io.Reader) (NGSFilter, error) {
-	ngsfilter := make(NGSFilter, 10)
+func ReadNGSFilter(reader io.Reader) (obingslibrary.NGSLibrary, error) {
+	ngsfilter := obingslibrary.MakeNGSLibrary()
 
 	lines := _readLines(reader)
 
-	for _, line := range lines {
+	for i, line := range lines {
 		line = strings.TrimSpace(line)
 
 		if strings.HasPrefix(line, "#") || len(line) == 0 {
@@ -100,33 +90,25 @@ func ReadNGSFilter(reader io.Reader) (NGSFilter, error) {
 		split := strings.SplitN(line, "@", 2)
 
 		primers, tags, experiment, sample, partial := _parseMainNGSFilter(split[0])
-		newPCR := PCR{
-			Experiment:  experiment,
-			Sample:      sample,
-			Partial:     partial,
-			Annotations: nil,
-		}
 
-		if len(split) > 1 && len(split[1]) > 0 {
-			newPCR.Annotations = obiseq.GetAnnotation()
-			ParseOBIFeatures(split[1], newPCR.Annotations)
-		}
-
-		samples, ok := ngsfilter[primers]
+		marker, _ := ngsfilter.GetMarker(primers.Forward, primers.Reverse)
+		pcr, ok := marker.GetPCR(tags.Forward, tags.Reverse)
 
 		if ok {
-			pcr, ok := samples[tags]
-
-			if ok {
-				return nil, fmt.Errorf("pair of tags %v used for samples %s in %s and %s in %s",
-					tags, sample, experiment, pcr.Sample, pcr.Experiment)
-			}
-
-			samples[tags] = newPCR
-		} else {
-			ngsfilter[primers] = make(PCRs, 1000)
-			ngsfilter[primers][tags] = newPCR
+			return ngsfilter,
+				fmt.Errorf("line %d : tag pair (%s,%s) used more than once with marker (%s,%s)",
+					i, tags.Forward, tags.Reverse, primers.Forward, primers.Reverse)
 		}
+
+		pcr.Experiment = experiment
+		pcr.Sample = sample
+		pcr.Partial = partial
+
+		if len(split) > 1 && len(split[1]) > 0 {
+			pcr.Annotations = make(obiseq.Annotation)
+			ParseOBIFeatures(split[1], pcr.Annotations)
+		}
+
 	}
 
 	return ngsfilter, nil