mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
Adds option to tune the pairing of the sequences in obipairing and some stats to the results
Former-commit-id: a6cf9cb4d4ab20a433a2534fd7d11cd3ca8ebbaa
This commit is contained in:
@ -351,8 +351,8 @@ func PERightAlign(seqA, seqB *obiseq.BioSequence, gap float64,
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}
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func PEAlign(seqA, seqB *obiseq.BioSequence,
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gap float64, delta int,
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arena PEAlignArena) (int, []int, int, int) {
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gap float64, fastAlign bool, delta int, fastScoreRel bool,
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arena PEAlignArena) (int, []int, int, int, float64) {
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var score, shift int
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var startA, startB int
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var partLen, over int
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@ -365,107 +365,143 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
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_InitDNAScoreMatrix()
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}
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index := obikmer.Index4mer(seqA,
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&arena.pointer.fastIndex,
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&arena.pointer.fastBuffer)
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fastCount := -1
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fastScore := -1.0
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shift, fastScore := obikmer.FastShiftFourMer(index, seqB, nil)
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if fastAlign {
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if shift > 0 {
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over = seqA.Len() - shift
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} else {
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over = seqB.Len() + shift
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}
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index := obikmer.Index4mer(seqA,
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&arena.pointer.fastIndex,
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&arena.pointer.fastBuffer)
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// At least one mismatch exists in the overlaping region
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if fastScore+3 < over {
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shift, fastCount, fastScore = obikmer.FastShiftFourMer(index, seqA.Len(), seqB, fastScoreRel, nil)
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if shift > 0 {
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startA = shift - delta
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if startA < 0 {
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startA = 0
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}
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extra5 = -startA
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startB = 0
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over = seqA.Len() - shift
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} else {
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over = seqB.Len() + shift
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}
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rawSeqA = seqA.Sequence()[startA:]
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qualSeqA = seqA.Qualities()[startA:]
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partLen = len(rawSeqA)
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if partLen > seqB.Len() {
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partLen = seqB.Len()
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// At least one mismatch exists in the overlaping region
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if fastCount+3 < over {
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if shift > 0 {
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startA = shift - delta
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if startA < 0 {
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startA = 0
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}
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extra5 = -startA
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startB = 0
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rawSeqA = seqA.Sequence()[startA:]
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qualSeqA = seqA.Qualities()[startA:]
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partLen = len(rawSeqA)
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if partLen > seqB.Len() {
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partLen = seqB.Len()
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}
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rawSeqB = seqB.Sequence()[0:partLen]
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qualSeqB = seqB.Qualities()[0:partLen]
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extra3 = seqB.Len() - partLen
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score = _FillMatrixPeLeftAlign(
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rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
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&arena.pointer.scoreMatrix,
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&arena.pointer.pathMatrix)
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} else {
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startA = 0
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startB = -shift - delta
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if startB < 0 {
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startB = 0
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}
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extra5 = startB
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rawSeqB = seqB.Sequence()[startB:]
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qualSeqB = seqB.Qualities()[startB:]
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partLen = len(rawSeqB)
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if partLen > seqA.Len() {
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partLen = seqA.Len()
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}
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rawSeqA = seqA.Sequence()[:partLen]
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qualSeqA = seqA.Qualities()[:partLen]
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extra3 = partLen - seqA.Len()
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score = _FillMatrixPeRightAlign(
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rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
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&arena.pointer.scoreMatrix,
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&arena.pointer.pathMatrix)
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}
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rawSeqB = seqB.Sequence()[0:partLen]
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qualSeqB = seqB.Qualities()[0:partLen]
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extra3 = seqB.Len() - partLen
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score = _FillMatrixPeLeftAlign(
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rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
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&arena.pointer.scoreMatrix,
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&arena.pointer.pathMatrix)
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arena.pointer.path = _Backtracking(arena.pointer.pathMatrix,
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len(rawSeqA), len(rawSeqB),
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&arena.pointer.path)
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} else {
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startA = 0
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startB = -shift - delta
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if startB < 0 {
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startB = 0
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}
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extra5 = startB
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rawSeqB = seqB.Sequence()[startB:]
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qualSeqB = seqB.Qualities()[startB:]
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partLen = len(rawSeqB)
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if partLen > seqA.Len() {
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partLen = seqA.Len()
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}
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rawSeqA = seqA.Sequence()[:partLen]
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qualSeqA = seqA.Qualities()[:partLen]
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extra3 = partLen - seqA.Len()
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// Both overlaping regions are identicals
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score = _FillMatrixPeRightAlign(
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rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
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&arena.pointer.scoreMatrix,
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&arena.pointer.pathMatrix)
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if shift > 0 {
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startA = shift
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startB = 0
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extra5 = -startA
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qualSeqA = seqA.Qualities()[startA:]
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partLen = len(qualSeqA)
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qualSeqB = seqB.Qualities()[0:partLen]
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extra3 = seqB.Len() - partLen
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score = 0
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} else {
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startA = 0
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startB = -shift
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extra5 = startB
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qualSeqB = seqB.Qualities()[startB:]
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partLen = len(qualSeqB)
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extra3 = partLen - seqA.Len()
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qualSeqA = seqA.Qualities()[:partLen]
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}
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score = 0
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for i, qualA := range qualSeqA {
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qualB := qualSeqB[i]
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score += _NucScorePartMatchMatch[qualA][qualB]
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}
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arena.pointer.path = arena.pointer.path[:0]
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arena.pointer.path = append(arena.pointer.path, 0, partLen)
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}
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arena.pointer.path[0] += extra5
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if arena.pointer.path[len(arena.pointer.path)-1] == 0 {
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arena.pointer.path[len(arena.pointer.path)-2] += extra3
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} else {
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arena.pointer.path = append(arena.pointer.path, extra3, 0)
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}
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} else {
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//
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// No Fast Heuristic
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//
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rawSeqA = seqA.Sequence()
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qualSeqA = seqA.Qualities()
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rawSeqB = seqB.Sequence()
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qualSeqB = seqB.Qualities()
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scoreR := _FillMatrixPeRightAlign(
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rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
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&arena.pointer.scoreMatrix,
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&arena.pointer.pathMatrix)
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arena.pointer.path = _Backtracking(arena.pointer.pathMatrix,
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len(rawSeqA), len(rawSeqB),
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&arena.pointer.path)
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} else {
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scoreL := _FillMatrixPeLeftAlign(
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rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
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&arena.pointer.scoreMatrix,
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&arena.pointer.pathMatrix)
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// Both overlaping regions are identicals
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if scoreL > scoreR {
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arena.pointer.path = _Backtracking(arena.pointer.pathMatrix,
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len(rawSeqA), len(rawSeqB),
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&arena.pointer.path)
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}
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if shift > 0 {
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startA = shift
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startB = 0
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extra5 = -startA
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qualSeqA = seqA.Qualities()[startA:]
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partLen = len(qualSeqA)
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qualSeqB = seqB.Qualities()[0:partLen]
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extra3 = seqB.Len() - partLen
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score = 0
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} else {
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startA = 0
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startB = -shift
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extra5 = startB
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qualSeqB = seqB.Qualities()[startB:]
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partLen = len(qualSeqB)
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extra3 = partLen - seqA.Len()
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qualSeqA = seqA.Qualities()[:partLen]
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}
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score = 0
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for i, qualA := range qualSeqA {
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qualB := qualSeqB[i]
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score += _NucScorePartMatchMatch[qualA][qualB]
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}
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arena.pointer.path = arena.pointer.path[:0]
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arena.pointer.path = append(arena.pointer.path, 0, partLen)
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}
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arena.pointer.path[0] += extra5
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if arena.pointer.path[len(arena.pointer.path)-1] == 0 {
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arena.pointer.path[len(arena.pointer.path)-2] += extra3
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} else {
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arena.pointer.path = append(arena.pointer.path, extra3, 0)
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}
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return score, arena.pointer.path, fastScore, over
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return score, arena.pointer.path, fastCount, over, fastScore
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}
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