Adds the option --pairing-scale to obipairing

Former-commit-id: c60416708467f5e818e70e08b3c512014b6212f0

pkg/obitools/obipairing/options.go

@@ -10,11 +10,12 @@ var _ForwardFile = ""
 var _ReverseFile = ""
 var _Delta = 5
 var _MinOverlap = 20
-var _GapPenality = float64(2.0)
+var _GapPenality = 2.0
 var _WithoutStats = false
 var _MinIdentity = 0.9
 var _NoFastAlign = false
 var _FastScoreAbs = false
+var _PenalityScale = 1.0
 
 func PairingOptionSet(options *getoptions.GetOpt) {
 	options.StringVar(&_ForwardFile, "forward-reads", "",
@@ -38,6 +39,8 @@ func PairingOptionSet(options *getoptions.GetOpt) {
 	options.Float64Var(&_GapPenality, "gap-penality", _GapPenality,
 		options.Alias("G"),
 		options.Description("Gap penality expressed as the multiply factor applied to the mismatch score between two nucleotides with a quality of 40 (default 2)."))
+	options.Float64Var(&_PenalityScale, "penality-scale", _PenalityScale,
+		options.Description("Scale factor applied to the mismatch score and the gap penality (default 1)."))
 	options.BoolVar(&_WithoutStats, "without-stat", _WithoutStats,
 		options.Alias("S"),
 		options.Description("Remove alignment statistics from the produced consensus sequences."))
@@ -85,6 +88,10 @@ func CLIGapPenality() float64 {
 	return _GapPenality
 }
 
+func CLIPenalityScale() float64 {
+	return _PenalityScale
+}
+
 func CLIWithStats() bool {
 	return !_WithoutStats
 }

pkg/obitools/obipairing/pairing.go

@@ -106,11 +106,14 @@ func JoinPairedSequence(seqA, seqB *obiseq.BioSequence, inplace bool) *obiseq.Bi
 // An obiseq.BioSequence corresponding to the assembling of the both
 // input sequence.
 func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
-	gap float64, delta, minOverlap int, minIdentity float64, withStats bool,
+	gap, scale float64, delta, minOverlap int, minIdentity float64, withStats bool,
 	inplace bool, fastAlign, fastModeRel bool,
 	arenaAlign obialign.PEAlignArena) *obiseq.BioSequence {
 
-	score, path, fastcount, over, fastscore := obialign.PEAlign(seqA, seqB, gap, fastAlign, delta, fastModeRel, arenaAlign)
+	score, path, fastcount, over, fastscore := obialign.PEAlign(seqA, seqB,
+		gap, scale,
+		fastAlign, delta, fastModeRel,
+		arenaAlign)
 	cons, match := obialign.BuildQualityConsensus(seqA, seqB, path, true)
 
 	left := path[0]
@@ -210,7 +213,7 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
 // The function returns an iterator over batches of obiseq.Biosequence object.
 // each pair of processed sequences produces one sequence in the result iterator.
 func IAssemblePESequencesBatch(iterator obiiter.IBioSequence,
-	gap float64, delta, minOverlap int,
+	gap, scale float64, delta, minOverlap int,
 	minIdentity float64, fastAlign, fastModeRel,
 	withStats bool, sizes ...int) obiiter.IBioSequence {
 
@@ -241,7 +244,9 @@ func IAssemblePESequencesBatch(iterator obiiter.IBioSequence,
 			cons := make(obiseq.BioSequenceSlice, len(batch.Slice()))
 			for i, A := range batch.Slice() {
 				B := A.PairedWith()
-				cons[i] = AssemblePESequences(A, B.ReverseComplement(true), gap, delta, minOverlap, minIdentity, withStats, true, fastAlign, fastModeRel, arena)
+				cons[i] = AssemblePESequences(A, B.ReverseComplement(true),
+					gap, scale,
+					delta, minOverlap, minIdentity, withStats, true, fastAlign, fastModeRel, arena)
 			}
 			newIter.Push(obiiter.MakeBioSequenceBatch(
 				batch.Order(),

pkg/obitools/obitagpcr/pcrtag.go

@@ -13,7 +13,7 @@ import (
 )
 
 func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
-	gap float64, delta, minOverlap int,
+	gap, scale float64, delta, minOverlap int,
 	minIdentity float64, fastAlign, fastScoreRel,
 	withStats bool) obiiter.IBioSequence {
 
@@ -50,7 +50,8 @@ func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
 				B := A.PairedWith()
 				consensus := obipairing.AssemblePESequences(
 					A.Copy(), B.ReverseComplement(false),
-					gap, delta, minOverlap, minIdentity, withStats, true,
+					gap, scale,
+					delta, minOverlap, minIdentity, withStats, true,
 					fastAlign, fastScoreRel, arena,
 				)