change the model for representing paired reads and extend its usage to other commands

pkg/obiseq/paired_reads.go

@@ -0,0 +1,58 @@
+package obiseq
+
+import log "github.com/sirupsen/logrus"
+
+func (s *BioSequence) IsPaired() bool {
+	return s.paired != nil
+}
+
+func (s *BioSequence) PairedWith() *BioSequence {
+	return s.paired
+}
+
+func (s *BioSequence) PairTo(p *BioSequence) {
+	s.paired = p
+	if p != nil {
+		p.paired = s
+	}
+}
+
+func (s *BioSequence) UnPair() {
+	if s.paired != nil {
+		s.paired.paired = nil
+	}
+	s.paired = nil
+}
+
+func (s *BioSequenceSlice) IsPaired() bool {
+	return (*s)[0].paired != nil
+}
+
+func (s *BioSequenceSlice) PairedWith() *BioSequenceSlice {
+	ps := NewBioSequenceSlice(len(*s))
+	for i, seq := range *s {
+		(*ps)[i] = seq.PairedWith()
+	}
+
+	return ps
+}
+
+func (s *BioSequenceSlice) PairTo(p *BioSequenceSlice) {
+
+	if len(*s) != len(*p) {
+		log.Fatalf("Pairing of iterators: both batches have not the same length : (%d,%d)",
+			len(*s), len(*p),
+		)
+	}
+
+	for i, seq := range *s {
+		seq.PairTo((*p)[i])
+	}
+
+}
+
+func (s *BioSequenceSlice) UnPair() {
+	for _, seq := range *s {
+		seq.UnPair()
+	}
+}