Finalyse the obimultiplex with indels

Former-commit-id: cef0ac39dac0e02d16d4bd321966a0f8a67f2c85

pkg/obialign/fastlcsegf.go

@@ -49,6 +49,10 @@ func FastLCSEGFScoreByte(bA, bB []byte, maxError int, endgapfree bool, buffer *[
 
 	delta := lA - lB
 
+	if endgapfree {
+		maxError += delta
+	}
+
 	// The difference of length is larger the maximum allowed errors
 	if delta > maxError {
 		return -1, -1
@@ -170,6 +174,9 @@ func FastLCSEGFScoreByte(bA, bB []byte, maxError int, endgapfree bool, buffer *[
 			// 	score = _setout(score)
 			// }
 
+			if x == 0 || x == (even-1) {
+				score = _setout(score)
+			}
 			// // BEGINNING OF DEBUG CODE //
 			// if i < 2 && j < 5 {
 			// 	log.Debugf("[%d,%d]\n",i,j)

pkg/obiapat/pattern.go

@@ -370,10 +370,11 @@ func (pattern ApatPattern) BestMatch(sequence ApatSequence, begin, length int) (
 	score, lali := obialign.FastLCSEGFScoreByte(
 		(*cseq)[start:end],
 		(*cpattern)[0:int(pattern.pointer.pointer.patlen)],
-		nerr*2, true, &buffer)
+		nerr, true, &buffer)
 
 	nerr = lali - score
 	start = best[0] + int(pattern.pointer.pointer.patlen) - lali
+	end = start + lali 
 	log.Println("results", score, lali, start, nerr)
 	return
 }

pkg/obingslibrary/match.go

@@ -199,7 +199,7 @@ func (marker *Marker) Match(sequence *obiseq.BioSequence) *DemultiplexMatch {
 
 			m.ForwardMatch = direct.String()
 			m.ForwardTag = sftag
-			m.ReverseMismatches = nerr
+			m.ForwardMismatches = nerr
 			m.BarcodeEnd = start
 
 			sample, ok := marker.samples[TagPair{sftag, rtag}]