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

pkg/obiseq/biosequence.go

@@ -55,6 +55,7 @@ type BioSequence struct {
 	sequence    []byte // The sequence itself, it is accessible by the methode Sequence
 	qualities   []byte // The quality scores of the sequence.
 	feature     []byte
+	paired      *BioSequence // A pointer to the paired sequence
 	annotations Annotation
 }
 
@@ -69,6 +70,7 @@ func MakeEmptyBioSequence() BioSequence {
 		sequence:    nil,
 		qualities:   nil,
 		feature:     nil,
+		paired:      nil,
 		annotations: nil,
 	}
 }
@@ -275,3 +277,4 @@ func (s *BioSequence) WriteByte(data byte) error {
 func (s *BioSequence) Clear() {
 	s.sequence = s.sequence[0:0]
 }
+

pkg/obiseq/biosequenceslice.go

@@ -23,7 +23,7 @@ func NewBioSequenceSlice(size ...int) *BioSequenceSlice {
 	slice := _BioSequenceSlicePool.Get().(*BioSequenceSlice)
 	if len(size) > 0 {
 		s := size[0]
-		slice.InsureCapacity(s)
+		slice = slice.InsureCapacity(s)
 		(*slice)=(*slice)[0:s]
 	}
 	return slice

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()
+	}
+}

pkg/obiseq/predicate.go

@@ -11,6 +11,61 @@ import (
 
 type SequencePredicate func(*BioSequence) bool
 
+type SeqPredicateMode int
+
+const (
+	ForwardOnly SeqPredicateMode = iota
+	ReverseOnly
+	And
+	Or
+	AndNot
+	Xor
+)
+
+func (predicate SequencePredicate) PredicateOnPaired(ifnotpaired bool) SequencePredicate {
+	if predicate == nil {
+		return nil
+	}
+
+	p := func(sequence *BioSequence) bool {
+		if sequence.IsPaired() {
+			return predicate(sequence.PairedWith())
+		}
+		return ifnotpaired
+	}
+
+	return p
+}
+
+func (predicate SequencePredicate) PairedPredicat(mode SeqPredicateMode) SequencePredicate {
+	if predicate == nil {
+		return nil
+	}
+
+	p := func(sequence *BioSequence) bool {
+		good := predicate(sequence)
+
+		if sequence.IsPaired() && mode != ForwardOnly {
+			pgood := predicate(sequence.PairedWith())
+			switch mode {
+			case ReverseOnly:
+				good = pgood
+			case And:
+				good = good && pgood
+			case Or:
+				good = good || pgood
+			case AndNot:
+				good = good && !pgood
+			case Xor:
+				good = (good || pgood) && !(good && pgood)
+			}
+		}
+		return good
+	}
+
+	return p
+}
+
 func (predicate1 SequencePredicate) And(predicate2 SequencePredicate) SequencePredicate {
 	switch {
 	case predicate1 == nil:
@@ -209,8 +264,8 @@ func ExpressionPredicat(expression string) SequencePredicate {
 	f := func(sequence *BioSequence) bool {
 		value, err := exp.EvalBool(context.Background(),
 			map[string]interface{}{
-				"annotations":     sequence.Annotations(),
-				"sequence":  sequence,
+				"annotations": sequence.Annotations(),
+				"sequence":    sequence,
 			},
 		)
 
@@ -225,4 +280,3 @@ func ExpressionPredicat(expression string) SequencePredicate {
 
 	return f
 }
-