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Adds the option --pairing-scale to obipairing

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Former-commit-id: c60416708467f5e818e70e08b3c512014b6212f0
This commit is contained in:
Eric Coissac
2023-12-07 12:28:16 +01:00
parent 008f33aee4
commit 37c3e16d5d
6 changed files with 42 additions and 27 deletions
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40
pkg/obialign/pairedendalign.go
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@ -111,17 +111,17 @@ func _GetMatrixFrom(matrix *[]int, lenA, a, b int) (int, int, int) {
return m[i_left], m[i_diag], m[i_top]
}
func _PairingScorePeAlign(baseA, qualA, baseB, qualB byte) int {
func _PairingScorePeAlign(baseA, qualA, baseB, qualB byte, scale float64) int {
partMatch := _NucPartMatch[baseA&31][baseB&31]
// log.Printf("id : %f A : %s %d B : %s %d\n", part_match, string(baseA), qualA, string(baseB), qualB)
switch int(partMatch * 100) {
case 100:
return _NucScorePartMatchMatch[qualA][qualB]
case 0:
return _NucScorePartMatchMismatch[qualA][qualB]
return int(float64(_NucScorePartMatchMismatch[qualA][qualB])*scale + 0.5)
default:
return int(partMatch*float64(_NucScorePartMatchMatch[qualA][qualB]) +
(1-partMatch)*float64(_NucScorePartMatchMismatch[qualA][qualB]) +
(1-partMatch)*float64(_NucScorePartMatchMismatch[qualA][qualB])*scale +
0.5)
}
}
@ -135,7 +135,7 @@ func _PairingScorePeAlign(baseA, qualA, baseB, qualB byte) int {
// - 0 : for diagonal
// - -1 : for top
// - +1 : for left
func _FillMatrixPeLeftAlign(seqA, qualA, seqB, qualB []byte, gap float64,
func _FillMatrixPeLeftAlign(seqA, qualA, seqB, qualB []byte, gap, scale float64,
scoreMatrix, pathMatrix *[]int) int {
la := len(seqA)
@ -143,7 +143,7 @@ func _FillMatrixPeLeftAlign(seqA, qualA, seqB, qualB []byte, gap float64,
// The actual gap score is the gap score times the mismatch between
// two bases with a score of 40
gapPenalty := int(gap * float64(_NucScorePartMatchMismatch[40][40]))
gapPenalty := int(scale*gap*float64(_NucScorePartMatchMismatch[40][40]) + 0.5)
needed := (la + 1) * (lb + 1)
@ -177,7 +177,7 @@ func _FillMatrixPeLeftAlign(seqA, qualA, seqB, qualB []byte, gap float64,
left, diag, top := _GetMatrixFrom(scoreMatrix, la, i, j)
// log.Infof("LA: i : %d j : %d left : %d diag : %d top : %d\n", i, j, left, diag, top)
diag += _PairingScorePeAlign(seqA[i], qualA[i], seqB[j], qualB[j])
diag += _PairingScorePeAlign(seqA[i], qualA[i], seqB[j], qualB[j], scale)
left += gapPenalty
top += gapPenalty
@ -195,7 +195,7 @@ func _FillMatrixPeLeftAlign(seqA, qualA, seqB, qualB []byte, gap float64,
// Special case for the last line Left gap are free
left, diag, top := _GetMatrixFrom(scoreMatrix, la, la1, j)
diag += _PairingScorePeAlign(seqA[la1], qualA[la1], seqB[j], qualB[j])
diag += _PairingScorePeAlign(seqA[la1], qualA[la1], seqB[j], qualB[j], scale)
top += gapPenalty
switch {
@ -218,7 +218,7 @@ func _FillMatrixPeLeftAlign(seqA, qualA, seqB, qualB []byte, gap float64,
// With A spanning over lines and B over columns
// - First line gap = 0
// - Last column gaps = 0
func _FillMatrixPeRightAlign(seqA, qualA, seqB, qualB []byte, gap float64,
func _FillMatrixPeRightAlign(seqA, qualA, seqB, qualB []byte, gap, scale float64,
scoreMatrix, pathMatrix *[]int) int {
la := len(seqA)
@ -226,7 +226,7 @@ func _FillMatrixPeRightAlign(seqA, qualA, seqB, qualB []byte, gap float64,
// The actual gap score is the gap score times the mismatch between
// two bases with a score of 40
gapPenalty := int(gap * float64(_NucScorePartMatchMismatch[40][40]))
gapPenalty := int(scale*gap*float64(_NucScorePartMatchMismatch[40][40]) + 0.5)
needed := (la + 1) * (lb + 1)
@ -259,7 +259,7 @@ func _FillMatrixPeRightAlign(seqA, qualA, seqB, qualB []byte, gap float64,
for i := 0; i < la; i++ {
left, diag, top := _GetMatrixFrom(scoreMatrix, la, i, j)
diag += _PairingScorePeAlign(seqA[i], qualA[i], seqB[j], qualB[j])
diag += _PairingScorePeAlign(seqA[i], qualA[i], seqB[j], qualB[j], scale)
left += gapPenalty
top += gapPenalty
@ -283,7 +283,7 @@ func _FillMatrixPeRightAlign(seqA, qualA, seqB, qualB []byte, gap float64,
for i := 0; i < la; i++ {
left, diag, top := _GetMatrixFrom(scoreMatrix, la, i, lb1)
diag += _PairingScorePeAlign(seqA[i], qualA[i], seqB[lb1], qualB[lb1])
diag += _PairingScorePeAlign(seqA[i], qualA[i], seqB[lb1], qualB[lb1], scale)
left += gapPenalty
// log.Infof("LR: i : %d j : %d left : %d diag : %d top : %d [%d]\n", i, lb1, left, diag, top, _GetMatrix(scoreMatrix, la, i, lb1))
@ -302,7 +302,7 @@ func _FillMatrixPeRightAlign(seqA, qualA, seqB, qualB []byte, gap float64,
}
func PELeftAlign(seqA, seqB *obiseq.BioSequence, gap float64,
func PELeftAlign(seqA, seqB *obiseq.BioSequence, gap, scale float64,
arena PEAlignArena) (int, []int) {
if !_InitializedDnaScore {
@ -315,7 +315,7 @@ func PELeftAlign(seqA, seqB *obiseq.BioSequence, gap float64,
}
score := _FillMatrixPeLeftAlign(seqA.Sequence(), seqA.Qualities(),
seqB.Sequence(), seqB.Qualities(), gap,
seqB.Sequence(), seqB.Qualities(), gap, scale,
&arena.pointer.scoreMatrix,
&arena.pointer.pathMatrix)
@ -326,7 +326,7 @@ func PELeftAlign(seqA, seqB *obiseq.BioSequence, gap float64,
return score, arena.pointer.path
}
func PERightAlign(seqA, seqB *obiseq.BioSequence, gap float64,
func PERightAlign(seqA, seqB *obiseq.BioSequence, gap, scale float64,
arena PEAlignArena) (int, []int) {
if !_InitializedDnaScore {
@ -339,7 +339,7 @@ func PERightAlign(seqA, seqB *obiseq.BioSequence, gap float64,
}
score := _FillMatrixPeRightAlign(seqA.Sequence(), seqA.Qualities(),
seqB.Sequence(), seqB.Qualities(), gap,
seqB.Sequence(), seqB.Qualities(), gap, scale,
&arena.pointer.scoreMatrix,
&arena.pointer.pathMatrix)
@ -351,7 +351,7 @@ func PERightAlign(seqA, seqB *obiseq.BioSequence, gap float64,
}
func PEAlign(seqA, seqB *obiseq.BioSequence,
gap float64, fastAlign bool, delta int, fastScoreRel bool,
gap, scale float64, fastAlign bool, delta int, fastScoreRel bool,
arena PEAlignArena) (int, []int, int, int, float64) {
var score, shift int
var startA, startB int
@ -403,7 +403,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
qualSeqB = seqB.Qualities()[0:partLen]
extra3 = seqB.Len() - partLen
score = _FillMatrixPeLeftAlign(
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap, scale,
&arena.pointer.scoreMatrix,
&arena.pointer.pathMatrix)
} else {
@ -425,7 +425,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
extra3 = partLen - seqA.Len()
score = _FillMatrixPeRightAlign(
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap, scale,
&arena.pointer.scoreMatrix,
&arena.pointer.pathMatrix)
}
@ -482,7 +482,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
qualSeqB = seqB.Qualities()
scoreR := _FillMatrixPeRightAlign(
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap, scale,
&arena.pointer.scoreMatrix,
&arena.pointer.pathMatrix)
@ -491,7 +491,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
&arena.pointer.path)
scoreL := _FillMatrixPeLeftAlign(
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap, scale,
&arena.pointer.scoreMatrix,
&arena.pointer.pathMatrix)