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Rename the Length methods Len to follow GO standart

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This commit is contained in:
Eric Coissac
2022-11-17 11:09:58 +01:00
parent eb32089305
commit 29563aa94e
30 changed files with 134 additions and 130 deletions
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25
pkg/obialign/pairedendalign.go
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@ -229,7 +229,7 @@ func PELeftAlign(seqA, seqB *obiseq.BioSequence, gap float64,
}
if arena.pointer == nil {
arena = MakePEAlignArena(seqA.Length(), seqB.Length())
arena = MakePEAlignArena(seqA.Len(), seqB.Len())
}
score := _FillMatrixPeLeftAlign(seqA.Sequence(), seqA.Qualities(),
@ -238,7 +238,7 @@ func PELeftAlign(seqA, seqB *obiseq.BioSequence, gap float64,
&arena.pointer.pathMatrix)
arena.pointer.path = _Backtracking(arena.pointer.pathMatrix,
seqA.Length(), seqB.Length(),
seqA.Len(), seqB.Len(),
&arena.pointer.path)
return score, arena.pointer.path
@ -253,7 +253,7 @@ func PERightAlign(seqA, seqB *obiseq.BioSequence, gap float64,
}
if arena.pointer == nil {
arena = MakePEAlignArena(seqA.Length(), seqB.Length())
arena = MakePEAlignArena(seqA.Len(), seqB.Len())
}
score := _FillMatrixPeRightAlign(seqA.Sequence(), seqA.Qualities(),
@ -262,7 +262,7 @@ func PERightAlign(seqA, seqB *obiseq.BioSequence, gap float64,
&arena.pointer.pathMatrix)
arena.pointer.path = _Backtracking(arena.pointer.pathMatrix,
seqA.Length(), seqB.Length(),
seqA.Len(), seqB.Len(),
&arena.pointer.path)
return score, arena.pointer.path
@ -290,15 +290,12 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
shift, fastScore := obikmer.FastShiftFourMer(index, seqB, nil)
if shift > 0 {
over = seqA.Length() - shift
over = seqA.Len() - shift
} else {
over = seqB.Length() + shift
over = seqB.Len() + shift
}
// log.Println(seqA.String())
// log.Println(seqB.String())
// log.Printf("Shift : %d Score : %d Over : %d La : %d:%d Lb: %d:%d\n", shift, fastScore, over, seqA.Length(), len(seqA.Qualities()), seqB.Length(), len(seqB.Qualities()))
if fastScore+3 < over {
// At least one mismatch exists in the overlaping region
@ -315,7 +312,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
partLen = len(rawSeqA)
rawSeqB = seqB.Sequence()[0:partLen]
qualSeqB = seqB.Qualities()[0:partLen]
extra3 = seqB.Length() - partLen
extra3 = seqB.Len() - partLen
score = _FillMatrixPeLeftAlign(
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
&arena.pointer.scoreMatrix,
@ -335,7 +332,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
partLen = len(rawSeqB)
rawSeqA = seqA.Sequence()[:partLen]
qualSeqA = seqA.Qualities()[:partLen]
extra3 = partLen - seqA.Length()
extra3 = partLen - seqA.Len()
score = _FillMatrixPeRightAlign(
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
&arena.pointer.scoreMatrix,
@ -354,7 +351,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
qualSeqA = seqA.Qualities()[startA:]
partLen = len(qualSeqA)
qualSeqB = seqB.Qualities()[0:partLen]
extra3 = seqB.Length() - partLen
extra3 = seqB.Len() - partLen
score = 0
} else {
startA = 0
@ -362,7 +359,7 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
extra5 = startB
qualSeqB = seqB.Qualities()[startB:]
partLen = len(qualSeqB)
extra3 = partLen - seqA.Length()
extra3 = partLen - seqA.Len()
qualSeqA = seqA.Qualities()[:partLen]
}
score = 0