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Changes to be committed:

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modified:   Release-notes.md
	modified:   pkg/obialign/pairedendalign.go
	modified:   pkg/obilua/obiseq.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/biosequence.go
	modified:   pkg/obitools/obipairing/pairing.go
This commit is contained in:
Eric Coissac
2024-11-27 09:56:22 +01:00
parent 7884a74f9c
commit d29a56dcbf
6 changed files with 78 additions and 29 deletions
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13
pkg/obialign/pairedendalign.go
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@ -485,7 +485,8 @@ func PECenterAlign(seqA, seqB *obiseq.BioSequence, gap, scale float64,
func PEAlign(seqA, seqB *obiseq.BioSequence,
gap, scale float64, fastAlign bool, delta int, fastScoreRel bool,
arena PEAlignArena, shift_buff *map[int]int) (int, []int, int, int, float64) {
arena PEAlignArena, shift_buff *map[int]int) (bool, int, []int, int, int, float64) {
var isLeftAlign bool
var score, shift int
var startA, startB int
var partLen, over int
@ -536,6 +537,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
rawSeqB = seqB.Sequence()[0:partLen]
qualSeqB = seqB.Qualities()[0:partLen]
extra3 = seqB.Len() - partLen
isLeftAlign = true
score = _FillMatrixPeLeftAlign(
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap, scale,
&arena.pointer.scoreMatrix,
@ -557,7 +559,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
rawSeqA = seqA.Sequence()[:partLen]
qualSeqA = seqA.Qualities()[:partLen]
extra3 = partLen - seqA.Len()
isLeftAlign = false
score = _FillMatrixPeRightAlign(
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap, scale,
&arena.pointer.scoreMatrix,
@ -581,6 +583,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
qualSeqB = seqB.Qualities()[0:partLen]
extra3 = seqB.Len() - partLen
score = 0
isLeftAlign = true
} else {
startA = 0
startB = -shift
@ -589,6 +592,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
partLen = len(qualSeqB)
extra3 = partLen - seqA.Len()
qualSeqA = seqA.Qualities()[:partLen]
isLeftAlign = false
}
score = 0
for i, qualA := range qualSeqA {
@ -625,6 +629,8 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
len(rawSeqA), len(rawSeqB),
&(arena.pointer.path))
isLeftAlign = false
scoreL := _FillMatrixPeLeftAlign(
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap, scale,
&arena.pointer.scoreMatrix,
@ -634,9 +640,10 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
path = _Backtracking(arena.pointer.pathMatrix,
len(rawSeqA), len(rawSeqB),
&(arena.pointer.path))
isLeftAlign = true
}
}
return score, path, fastCount, over, fastScore
return isLeftAlign, score, path, fastCount, over, fastScore
}