Adds the command obimultiplex

pkg/obingslibrary/ngslibrary.go

@@ -0,0 +1,65 @@
+package obingslibrary
+
+import (
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
+	"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 Marker struct {
+	forward   obiapat.ApatPattern
+	cforward  obiapat.ApatPattern
+	reverse   obiapat.ApatPattern
+	creverse  obiapat.ApatPattern
+	taglength int
+	samples   map[TagPair]*PCR
+}
+type NGSLibrary map[PrimerPair]*Marker
+
+func MakeNGSLibrary() NGSLibrary {
+	return make(NGSLibrary, 10)
+}
+
+func (library *NGSLibrary) GetMarker(forward, reverse string) (*Marker, bool) {
+	pair := PrimerPair{forward, reverse}
+	marker, ok := (*library)[pair]
+
+	if ok {
+		return marker, true
+	}
+
+	m := Marker{samples: make(map[TagPair]*PCR, 1000)}
+	(*library)[pair] = &m
+
+	return &m, false
+}
+
+func (marker *Marker) GetPCR(forward, reverse string) (*PCR, bool) {
+	pair := TagPair{forward, reverse}
+	pcr, ok := marker.samples[pair]
+
+	if ok {
+		return pcr, ok
+	}
+
+	ipcr := PCR{}
+	marker.samples[pair] = &ipcr
+
+	return &ipcr, false
+}