Patch an aligment bug on obipairing

pkg/obiseq/biosequenceslice.go

@@ -19,13 +19,19 @@ var _BioSequenceSlicePool = sync.Pool{
 }
 
 // > This function returns a pointer to a new `BioSequenceSlice` object
-func NewBioSequenceSlice() *BioSequenceSlice {
-	return _BioSequenceSlicePool.Get().(*BioSequenceSlice)
+func NewBioSequenceSlice(size ...int) *BioSequenceSlice {
+	slice := _BioSequenceSlicePool.Get().(*BioSequenceSlice)
+	if len(size) > 0 {
+		s := size[0]
+		slice.InsureCapacity(s)
+		(*slice)=(*slice)[0:s]
+	}
+	return slice
 }
 
 // `MakeBioSequenceSlice()` returns a pointer to a new `BioSequenceSlice` struct
-func MakeBioSequenceSlice() BioSequenceSlice {
-	return *NewBioSequenceSlice()
+func MakeBioSequenceSlice(size ...int) BioSequenceSlice {
+	return *NewBioSequenceSlice(size...)
 }
 
 func (s *BioSequenceSlice) Recycle() {

pkg/obiseq/worker.go

@@ -5,6 +5,10 @@ type SeqAnnotator func(*BioSequence)
 type SeqWorker func(*BioSequence) *BioSequence
 type SeqSliceWorker func(BioSequenceSlice) BioSequenceSlice
 
+func NilSeqWorker(seq *BioSequence) *BioSequence {
+	return seq
+}
+
 func AnnotatorToSeqWorker(function SeqAnnotator) SeqWorker {
 	f := func(seq *BioSequence) *BioSequence {
 		function(seq)
@@ -14,14 +18,57 @@ func AnnotatorToSeqWorker(function SeqAnnotator) SeqWorker {
 }
 
 func SeqToSliceWorker(worker SeqWorker, inplace bool) SeqSliceWorker {
-	f := func(input BioSequenceSlice) BioSequenceSlice {
-		output := input
-		if (! inplace) {
-			output = MakeBioSequenceSlice() 
+	var f SeqSliceWorker
+
+	if worker == nil {
+		if inplace {
+			f = func(input BioSequenceSlice) BioSequenceSlice {
+				return input
+			}
+		} else  {
+			f = func(input BioSequenceSlice) BioSequenceSlice {
+				output := MakeBioSequenceSlice(len(input))
+				copy(output,input)
+				return output
+			}		
 		}
-			for i,s := range(input) {
+	} else {
+		f = func(input BioSequenceSlice) BioSequenceSlice {
+			output := input
+			if !inplace {
+				output = MakeBioSequenceSlice(len(input))
+			}
+			for i, s := range input {
 				output[i] = worker(s)
 			}
+	
+			return output
+		}	
+	}
+
+	return f
+}
+
+func SeqToSliceConditionalWorker(worker SeqWorker,
+	condition SequencePredicate,
+	inplace bool) SeqSliceWorker {
+
+	if condition == nil {
+		return SeqToSliceWorker(worker,inplace)
+	}
+
+	f := func(input BioSequenceSlice) BioSequenceSlice {
+		output := input
+		if !inplace {
+			output = MakeBioSequenceSlice(len(input))
+		}
+		for i, s := range input {
+			if condition(s) {
+				output[i] = worker(s)
+			} else {
+				output[i] = s
+			}
+		}
 
 		return output
 	}
@@ -29,3 +76,18 @@ func SeqToSliceWorker(worker SeqWorker, inplace bool) SeqSliceWorker {
 	return f
 }
 
+func (worker SeqWorker) ChainWorkers(next SeqWorker) SeqWorker {
+	if worker == nil {
+		return next
+	} else {
+		if next == nil {
+			return worker
+		}
+	} 
+
+	f := func(seq *BioSequence) *BioSequence {
+		return next(worker(seq))
+	}
+
+	return f
+}