Patch a bug on writing to stdout, and add clearer error on openning data files

pkg/obialign/readalign.go

@@ -0,0 +1,144 @@
+package obialign
+
+import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+)
+
+func ReadAlign(seqA, seqB *obiseq.BioSequence,
+	gap, scale float64, delta int, fastScoreRel bool,
+	arena PEAlignArena, shift_buff *map[int]int) (int, []int, int, int, float64, bool) {
+	var score, shift int
+	var startA, startB int
+	var partLen, over int
+	var rawSeqA, qualSeqA []byte
+	var rawSeqB, qualSeqB []byte
+	var extra5, extra3 int
+
+	var path []int
+
+	if !_InitializedDnaScore {
+		_InitDNAScoreMatrix()
+	}
+
+	fastCount := -1
+	fastScore := -1.0
+
+	directAlignment := true
+
+	index := obikmer.Index4mer(seqA,
+		&arena.pointer.fastIndex,
+		&arena.pointer.fastBuffer)
+
+	shift, fastCount, fastScore = obikmer.FastShiftFourMer(index, shift_buff, seqA.Len(), seqB, fastScoreRel, nil)
+
+	seqBR := seqB.ReverseComplement(false)
+	shiftR, fastCountR, fastScoreR := obikmer.FastShiftFourMer(index, shift_buff, seqA.Len(), seqBR, fastScoreRel, nil)
+
+	if fastCount < fastCountR {
+		shift = shiftR
+		fastCount = fastCountR
+		fastScore = fastScoreR
+		seqB = seqBR
+		directAlignment = false
+	}
+
+	if shift > 0 {
+		over = seqA.Len() - shift
+	} else {
+		over = seqB.Len() + shift
+	}
+
+	// At least one mismatch exists in the overlaping region
+	if fastCount+3 < over {
+
+		if shift > 0 {
+			startA = shift - delta
+			if startA < 0 {
+				startA = 0
+			}
+			extra5 = -startA
+			startB = 0
+
+			rawSeqA = seqA.Sequence()[startA:]
+			qualSeqA = seqA.Qualities()[startA:]
+			partLen = len(rawSeqA)
+			if partLen > seqB.Len() {
+				partLen = seqB.Len()
+			}
+			rawSeqB = seqB.Sequence()[0:partLen]
+			qualSeqB = seqB.Qualities()[0:partLen]
+			extra3 = seqB.Len() - partLen
+			score = _FillMatrixPeLeftAlign(
+				rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap, scale,
+				&arena.pointer.scoreMatrix,
+				&arena.pointer.pathMatrix)
+		} else {
+
+			startA = 0
+			startB = -shift - delta
+			if startB < 0 {
+				startB = 0
+			}
+			extra5 = startB
+			rawSeqB = seqB.Sequence()[startB:]
+			qualSeqB = seqB.Qualities()[startB:]
+			partLen = len(rawSeqB)
+			if partLen > seqA.Len() {
+				partLen = seqA.Len()
+			}
+			rawSeqA = seqA.Sequence()[:partLen]
+			qualSeqA = seqA.Qualities()[:partLen]
+			extra3 = partLen - seqA.Len()
+
+			score = _FillMatrixPeRightAlign(
+				rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap, scale,
+				&arena.pointer.scoreMatrix,
+				&arena.pointer.pathMatrix)
+		}
+
+		path = _Backtracking(arena.pointer.pathMatrix,
+			len(rawSeqA), len(rawSeqB),
+			&arena.pointer.path)
+
+	} else {
+
+		// Both overlaping regions are identicals
+
+		if shift > 0 {
+			startA = shift
+			startB = 0
+			extra5 = -startA
+			qualSeqA = seqA.Qualities()[startA:]
+			partLen = len(qualSeqA)
+			qualSeqB = seqB.Qualities()[0:partLen]
+			extra3 = seqB.Len() - partLen
+			score = 0
+		} else {
+			startA = 0
+			startB = -shift
+			extra5 = startB
+			qualSeqB = seqB.Qualities()[startB:]
+			partLen = len(qualSeqB)
+			extra3 = partLen - seqA.Len()
+			qualSeqA = seqA.Qualities()[:partLen]
+		}
+		score = 0
+		for i, qualA := range qualSeqA {
+			qualB := qualSeqB[i]
+			score += _NucScorePartMatchMatch[qualA][qualB]
+		}
+
+		path = arena.pointer.path[:0]
+		path = append(path, 0, partLen)
+	}
+
+	path[0] += extra5
+	if path[len(path)-1] == 0 {
+		path[len(path)-2] += extra3
+	} else {
+		path = append(path, extra3, 0)
+	}
+
+	return score, path, fastCount, over, fastScore, directAlignment
+}