Adds option to tune the pairing of the sequences in obipairing and some stats to the results

Former-commit-id: a6cf9cb4d4ab20a433a2534fd7d11cd3ca8ebbaa

pkg/obitools/obipairing/options.go

@@ -13,6 +13,8 @@ var _MinOverlap = 20
 var _GapPenality = float64(2.0)
 var _WithoutStats = false
 var _MinIdentity = 0.9
+var _NoFastAlign = false
+var _FastScoreAbs = false
 
 func PairingOptionSet(options *getoptions.GetOpt) {
 	options.StringVar(&_ForwardFile, "forward-reads", "",
@@ -39,6 +41,10 @@ func PairingOptionSet(options *getoptions.GetOpt) {
 	options.BoolVar(&_WithoutStats, "without-stat", _WithoutStats,
 		options.Alias("S"),
 		options.Description("Remove alignment statistics from the produced consensus sequences."))
+	options.BoolVar(&_NoFastAlign, "exact-mode", _NoFastAlign,
+		options.Description("Do not run fast alignment heuristic."))
+	options.BoolVar(&_FastScoreAbs, "fast-absolute", _FastScoreAbs,
+		options.Description("Compute absolute fast score (no action in exact mode)."))
 }
 
 func OptionSet(options *getoptions.GetOpt) {
@@ -82,3 +88,11 @@ func CLIGapPenality() float64 {
 func CLIWithStats() bool {
 	return !_WithoutStats
 }
+
+func CLIFastMode() bool {
+	return !_NoFastAlign
+}
+
+func CLIFastRelativeScore() bool {
+	return !_FastScoreAbs
+}

pkg/obitools/obipairing/pairing.go

@@ -99,16 +99,18 @@ func JoinPairedSequence(seqA, seqB *obiseq.BioSequence, inplace bool) *obiseq.Bi
 // destroyed during the assembling process and cannot be reuse later on.
 // the gap and delta parametters.
 //
+// - fastModeRel: if set to true, the FAST score mode is set to relative score
+//
 // # Returns
 //
 // 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,
-	inplace bool,
+	inplace bool, fastAlign, fastModeRel bool,
 	arenaAlign obialign.PEAlignArena) *obiseq.BioSequence {
 
-	score, path, fastscore, over := obialign.PEAlign(seqA, seqB, gap, delta, arenaAlign)
+	score, path, fastcount, over, fastscore := obialign.PEAlign(seqA, seqB, gap, fastAlign, delta, fastModeRel, arenaAlign)
 	cons, match := obialign.BuildQualityConsensus(seqA, seqB, path, true)
 
 	left := path[0]
@@ -123,8 +125,12 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
 		identity = 0
 	}
 	annot := cons.Annotations()
-	annot["paring_fast_score"] = fastscore
-	annot["paring_fast_overlap"] = over
+
+	if fastAlign {
+		annot["paring_fast_count"] = fastcount
+		annot["paring_fast_score"] = math.Round(fastscore*1000) / 1000
+		annot["paring_fast_overlap"] = over
+	}
 
 	if aliLength >= minOverlap && identity >= minIdentity {
 		annot["mode"] = "alignment"
@@ -205,7 +211,7 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
 // each pair of processed sequences produces one sequence in the result iterator.
 func IAssemblePESequencesBatch(iterator obiiter.IBioSequence,
 	gap float64, delta, minOverlap int,
-	minIdentity float64,
+	minIdentity float64, fastAlign, fastModeRel,
 	withStats bool, sizes ...int) obiiter.IBioSequence {
 
 	if !iterator.IsPaired() {
@@ -235,7 +241,7 @@ 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, arena)
+				cons[i] = AssemblePESequences(A, B.ReverseComplement(true), gap, delta, minOverlap, minIdentity, withStats, true, fastAlign, fastModeRel, arena)
 			}
 			newIter.Push(obiiter.MakeBioSequenceBatch(
 				batch.Order(),

pkg/obitools/obitagpcr/pcrtag.go

@@ -14,7 +14,7 @@ import (
 
 func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
 	gap float64, delta, minOverlap int,
-	minIdentity float64,
+	minIdentity float64, fastAlign, fastScoreRel,
 	withStats bool) obiiter.IBioSequence {
 
 	if !iterator.IsPaired() {
@@ -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, arena,
+					gap, delta, minOverlap, minIdentity, withStats, true,
+					fastAlign, fastScoreRel, arena,
 				)
 
 				consensus, err = ngsfilter.ExtractBarcode(consensus, true)