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Connect the command line options to the algorithm of obipairing

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This commit is contained in:
Eric Coissac
2022-01-16 17:30:30 +01:00
parent 576a9f4d2d
commit 64676db3f4
7 changed files with 89 additions and 43 deletions
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32
pkg/obialign/pairedendalign.go
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@ -72,7 +72,7 @@ func _PairingScorePeAlign(baseA, qualA, baseB, qualB byte) int {
}
}
func _FillMatrixPeLeftAlign(seqA, qualA, seqB, qualB []byte, gap int,
func _FillMatrixPeLeftAlign(seqA, qualA, seqB, qualB []byte, gap float64,
scoreMatrix, pathMatrix *[]int) int {
la := len(seqA)
@ -80,7 +80,7 @@ func _FillMatrixPeLeftAlign(seqA, qualA, seqB, qualB []byte, gap int,
// The actual gap score is the gap score times the mismatch between
// two bases with a score of 40
gap = gap * _NucScorePartMatchMismatch[40][40]
gapPenalty := int(gap * float64(_NucScorePartMatchMismatch[40][40]))
needed := (la + 1) * (lb + 1)
@ -106,13 +106,13 @@ func _FillMatrixPeLeftAlign(seqA, qualA, seqB, qualB []byte, gap int,
for j := 0; j < lb; j++ {
_SetMatrices(scoreMatrix, pathMatrix, la, -1, j, (j+1)*gap, 1)
_SetMatrices(scoreMatrix, pathMatrix, la, -1, j, (j+1)*gapPenalty, 1)
for i := 0; i < la1; i++ {
left, diag, top := _GetMatrixFrom(scoreMatrix, la, i, j)
diag += _PairingScorePeAlign(seqA[i], qualA[i], seqB[j], qualB[j])
left += gap
top += gap
left += gapPenalty
top += gapPenalty
switch {
case diag > left && diag > top:
_SetMatrices(scoreMatrix, pathMatrix, la, i, j, diag, 0)
@ -127,7 +127,7 @@ func _FillMatrixPeLeftAlign(seqA, qualA, seqB, qualB []byte, gap int,
left, diag, top := _GetMatrixFrom(scoreMatrix, la, la1, j)
diag += _PairingScorePeAlign(seqA[la1], qualA[la1], seqB[j], qualB[j])
top += gap
top += gapPenalty
switch {
case diag > left && diag > top:
@ -143,7 +143,7 @@ func _FillMatrixPeLeftAlign(seqA, qualA, seqB, qualB []byte, gap int,
return _GetMatrix(scoreMatrix, la, la1, lb-1)
}
func _FillMatrixPeRightAlign(seqA, qualA, seqB, qualB []byte, gap int,
func _FillMatrixPeRightAlign(seqA, qualA, seqB, qualB []byte, gap float64,
scoreMatrix, pathMatrix *[]int) int {
la := len(seqA)
@ -151,7 +151,7 @@ func _FillMatrixPeRightAlign(seqA, qualA, seqB, qualB []byte, gap int,
// The actual gap score is the gap score times the mismatch between
// two bases with a score of 40
gap = gap * _NucScorePartMatchMismatch[40][40]
gapPenalty := int(gap * float64(_NucScorePartMatchMismatch[40][40]))
needed := (la + 1) * (lb + 1)
@ -170,7 +170,7 @@ func _FillMatrixPeRightAlign(seqA, qualA, seqB, qualB []byte, gap int,
// Fills the first column with score 0
for i := 0; i < la; i++ {
_SetMatrices(scoreMatrix, pathMatrix, la, i, -1, (i+1)*gap, -1)
_SetMatrices(scoreMatrix, pathMatrix, la, i, -1, (i+1)*gapPenalty, -1)
}
lb1 := lb - 1
@ -183,8 +183,8 @@ func _FillMatrixPeRightAlign(seqA, qualA, seqB, qualB []byte, gap int,
left, diag, top := _GetMatrixFrom(scoreMatrix, la, i, j)
diag += _PairingScorePeAlign(seqA[i], qualA[i], seqB[j], qualB[j])
left += gap
top += gap
left += gapPenalty
top += gapPenalty
switch {
case diag > left && left > top:
@ -205,7 +205,7 @@ func _FillMatrixPeRightAlign(seqA, qualA, seqB, qualB []byte, gap int,
left, diag, top := _GetMatrixFrom(scoreMatrix, la, i, lb1)
diag += _PairingScorePeAlign(seqA[i], qualA[i], seqB[lb1], qualB[lb1])
left += gap
left += gapPenalty
switch {
case diag > left && diag > top:
@ -220,7 +220,8 @@ func _FillMatrixPeRightAlign(seqA, qualA, seqB, qualB []byte, gap int,
return _GetMatrix(scoreMatrix, la, la-1, lb1)
}
func PELeftAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (int, []int) {
func PELeftAlign(seqA, seqB obiseq.BioSequence, gap float64,
arena PEAlignArena) (int, []int) {
if !_InitializedDnaScore {
log.Println("Initializing the DNA Scoring matrix")
@ -243,7 +244,8 @@ func PELeftAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (in
return score, arena.pointer.path
}
func PERightAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (int, []int) {
func PERightAlign(seqA, seqB obiseq.BioSequence, gap float64,
arena PEAlignArena) (int, []int) {
if !_InitializedDnaScore {
log.Println("Initializing the DNA Scoring matrix")
@ -267,7 +269,7 @@ func PERightAlign(seqA, seqB obiseq.BioSequence, gap int, arena PEAlignArena) (i
}
func PEAlign(seqA, seqB obiseq.BioSequence,
gap, delta int,
gap float64, delta int,
arena PEAlignArena) (int, []int) {
var score, shift int
var startA, startB int