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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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12
pkg/obialign/alignment.go
View File

@ -73,10 +73,10 @@ func _BuildAlignment(seqA, seqB []byte, path []int, gap byte, bufferA, bufferB *
func BuildAlignment(seqA, seqB *obiseq.BioSequence,
path []int, gap byte) (*obiseq.BioSequence, *obiseq.BioSequence) {
bufferSA := obiseq.GetSlice(seqA.Length())
bufferSA := obiseq.GetSlice(seqA.Len())
defer obiseq.RecycleSlice(&bufferSA)
bufferSB := obiseq.GetSlice(seqB.Length())
bufferSB := obiseq.GetSlice(seqB.Len())
defer obiseq.RecycleSlice(&bufferSB)
_BuildAlignment(seqA.Sequence(), seqB.Sequence(), path, gap,
@ -117,12 +117,12 @@ func BuildAlignment(seqA, seqB *obiseq.BioSequence,
// return.
func BuildQualityConsensus(seqA, seqB *obiseq.BioSequence, path []int, statOnMismatch bool) (*obiseq.BioSequence, int) {
bufferSA := obiseq.GetSlice(seqA.Length())
bufferSB := obiseq.GetSlice(seqB.Length())
bufferSA := obiseq.GetSlice(seqA.Len())
bufferSB := obiseq.GetSlice(seqB.Len())
defer obiseq.RecycleSlice(&bufferSB)
bufferQA := obiseq.GetSlice(seqA.Length())
bufferQB := obiseq.GetSlice(seqB.Length())
bufferQA := obiseq.GetSlice(seqA.Len())
bufferQB := obiseq.GetSlice(seqB.Len())
defer obiseq.RecycleSlice(&bufferQB)
_BuildAlignment(seqA.Sequence(), seqB.Sequence(), path, ' ',

6
pkg/obialign/fastlcs.go
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@ -60,8 +60,8 @@ var _notavail = encodeValues(0, 30000, false)
func FastLCSScore(seqA, seqB *obiseq.BioSequence, maxError int, buffer *[]uint64) (int, int) {
lA := seqA.Length()
lB := seqB.Length()
lA := seqA.Len()
lB := seqB.Len()
// Ensure that A is the longest
if lA < lB {
@ -70,7 +70,7 @@ func FastLCSScore(seqA, seqB *obiseq.BioSequence, maxError int, buffer *[]uint64
}
if maxError == -1 {
maxError = lA*2
maxError = lA * 2
}
delta := lA - lB

2
pkg/obialign/fourbitsencode.go
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@ -58,7 +58,7 @@ var _FourBitsBaseDecode = []byte{
// A byte slice can be provided (buffer) to preveent allocation of a new
// memory chunk by th function.
func Encode4bits(seq *obiseq.BioSequence, buffer []byte) []byte {
length := seq.Length()
length := seq.Len()
rawseq := seq.Sequence()
if buffer == nil {

4
pkg/obialign/is_d0_or_d1.go
View File

@ -14,8 +14,8 @@ func D1Or0(seq1, seq2 *obiseq.BioSequence) (int, int, byte, byte) {
pos := -1
l1 := seq1.Length()
l2 := seq2.Length()
l1 := seq1.Len()
l2 := seq2.Len()
if abs(l1-l2) > 1 {
return -1, pos, 0, 0

25
pkg/obialign/pairedendalign.go
View File

@ -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