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

pkg/obiiter/paired.go

@@ -0,0 +1,95 @@
+package obiiter
+
+import (
+	"log"
+)
+
+func (b BioSequenceBatch) IsPaired() bool {
+	return b.slice.IsPaired()
+}
+
+func (b BioSequenceBatch) PairedWith() BioSequenceBatch {
+	return MakeBioSequenceBatch(b.order,
+		*b.slice.PairedWith())
+
+}
+
+func (b *BioSequenceBatch) PairTo(p *BioSequenceBatch) {
+
+	if b.order != p.order {
+		log.Fatalf("both batches are not synchronized : (%d,%d)",
+			b.order, p.order,
+		)
+	}
+
+	b.slice.PairTo(&p.slice)
+
+}
+
+func (b *BioSequenceBatch) UnPair() {
+	b.slice.UnPair()
+}
+
+func (iter IBioSequence) MarkAsPaired() {
+	iter.pointer.paired = true
+}
+
+func (iter IBioSequence) PairTo(p IBioSequence) IBioSequence {
+
+	newIter := MakeIBioSequence()
+
+	iter = iter.SortBatches()
+	p = p.SortBatches()
+
+	newIter.Add(1)
+
+	go func() {
+		newIter.WaitAndClose()
+	}()
+
+	go func() {
+
+		for iter.Next() {
+			p.Next()
+			batch := iter.Get()
+			pbatch := p.Get()
+			batch.PairTo(&pbatch)
+			newIter.Push(batch)
+		}
+
+		newIter.Done()
+	}()
+
+	newIter.MarkAsPaired()
+	return newIter
+
+}
+
+func (iter IBioSequence) PairedWith() IBioSequence {
+
+	newIter := MakeIBioSequence()
+
+	newIter.Add(1)
+
+	go func() {
+		newIter.WaitAndClose()
+	}()
+
+	go func() {
+
+		for iter.Next() {
+			batch := iter.Get().PairedWith()
+			newIter.Push(batch)
+		}
+
+		newIter.Done()
+	}()
+
+	newIter.MarkAsPaired()
+	return newIter
+
+}
+
+func (iter IBioSequence) IsPaired() bool {
+	return iter.pointer.paired
+}