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Former-commit-id: ab9b4723f1dcf79fe5c073fff4d86f4f6969edfd
This commit is contained in:
Eric Coissac
2024-06-23 00:36:08 +02:00
parent 93f9dcb95f
commit c1f03cb1f6
9 changed files with 80 additions and 32 deletions
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40
pkg/obialign/pairedendalign.go
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@@ -1,8 +1,6 @@
package obialign
import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
)
@@ -319,7 +317,6 @@ func PELeftAlign(seqA, seqB *obiseq.BioSequence, gap, scale float64,
arena PEAlignArena) (int, []int) {
if !_InitializedDnaScore {
log.Println("Initializing the DNA Scoring matrix")
_InitDNAScoreMatrix()
}
@@ -332,18 +329,17 @@ func PELeftAlign(seqA, seqB *obiseq.BioSequence, gap, scale float64,
&arena.pointer.scoreMatrix,
&arena.pointer.pathMatrix)
arena.pointer.path = _Backtracking(arena.pointer.pathMatrix,
path := _Backtracking(arena.pointer.pathMatrix,
seqA.Len(), seqB.Len(),
&arena.pointer.path)
return score, arena.pointer.path
return score, path
}
func PERightAlign(seqA, seqB *obiseq.BioSequence, gap, scale float64,
arena PEAlignArena) (int, []int) {
if !_InitializedDnaScore {
log.Println("Initializing the DNA Scoring matrix")
_InitDNAScoreMatrix()
}
@@ -356,11 +352,11 @@ func PERightAlign(seqA, seqB *obiseq.BioSequence, gap, scale float64,
&arena.pointer.scoreMatrix,
&arena.pointer.pathMatrix)
arena.pointer.path = _Backtracking(arena.pointer.pathMatrix,
path := _Backtracking(arena.pointer.pathMatrix,
seqA.Len(), seqB.Len(),
&arena.pointer.path)
return score, arena.pointer.path
return score, path
}
func PEAlign(seqA, seqB *obiseq.BioSequence,
@@ -373,8 +369,9 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
var rawSeqB, qualSeqB []byte
var extra5, extra3 int
var path []int
if !_InitializedDnaScore {
log.Println("Initializing the DNA Scoring matrix")
_InitDNAScoreMatrix()
}
@@ -443,7 +440,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
&arena.pointer.pathMatrix)
}
arena.pointer.path = _Backtracking(arena.pointer.pathMatrix,
path = _Backtracking(arena.pointer.pathMatrix,
len(rawSeqA), len(rawSeqB),
&arena.pointer.path)
@@ -474,15 +471,16 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
qualB := qualSeqB[i]
score += _NucScorePartMatchMatch[qualA][qualB]
}
arena.pointer.path = arena.pointer.path[:0]
arena.pointer.path = append(arena.pointer.path, 0, partLen)
path = arena.pointer.path[:0]
path = append(path, 0, partLen)
}
arena.pointer.path[0] += extra5
if arena.pointer.path[len(arena.pointer.path)-1] == 0 {
arena.pointer.path[len(arena.pointer.path)-2] += extra3
path[0] += extra5
if path[len(path)-1] == 0 {
path[len(path)-2] += extra3
} else {
arena.pointer.path = append(arena.pointer.path, extra3, 0)
path = append(path, extra3, 0)
}
} else {
//
@@ -499,9 +497,9 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
&arena.pointer.scoreMatrix,
&arena.pointer.pathMatrix)
arena.pointer.path = _Backtracking(arena.pointer.pathMatrix,
path = _Backtracking(arena.pointer.pathMatrix,
len(rawSeqA), len(rawSeqB),
&arena.pointer.path)
&(arena.pointer.path))
scoreL := _FillMatrixPeLeftAlign(
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap, scale,
@@ -509,12 +507,12 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
&arena.pointer.pathMatrix)
if scoreL > scoreR {
arena.pointer.path = _Backtracking(arena.pointer.pathMatrix,
path = _Backtracking(arena.pointer.pathMatrix,
len(rawSeqA), len(rawSeqB),
&arena.pointer.path)
&(arena.pointer.path))
}
}
return score, arena.pointer.path, fastCount, over, fastScore
return score, path, fastCount, over, fastScore
}