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Code reefactoring

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This commit is contained in:
Eric Coissac
2022-01-14 16:10:19 +01:00
parent 45a1765a03
commit ff40222902
13 changed files with 68 additions and 92 deletions
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62
pkg/obialign/pairedendalign.go
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@@ -272,9 +272,9 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
arena PEAlignArena) (int, []int) {
var score, shift int
var startA, startB int
var part_len, over int
var raw_seqA, qual_seqA []byte
var raw_seqB, qual_seqB []byte
var partLen, over int
var rawSeqA, qualSeqA []byte
var rawSeqB, qualSeqB []byte
var extra5, extra3 int
if !_InitializedDnaScore {
@@ -286,7 +286,7 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
&arena.pointer.fastIndex,
&arena.pointer.fastBuffer)
shift, fast_score := obikmer.FastShiftFourMer(index, seqB, nil)
shift, fastScore := obikmer.FastShiftFourMer(index, seqB, nil)
if shift > 0 {
over = seqA.Length() - shift
@@ -294,7 +294,7 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
over = seqB.Length() + shift
}
if fast_score+3 < over {
if fastScore+3 < over {
if shift > 0 {
startA = shift - delta
if startA < 0 {
@@ -302,14 +302,14 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
}
extra5 = -startA
startB = 0
raw_seqA = seqA.Sequence()[startA:]
qual_seqA = seqA.Qualities()[startA:]
part_len = len(raw_seqA)
raw_seqB = seqB.Sequence()[0:part_len]
qual_seqB = seqB.Qualities()[0:part_len]
extra3 = seqB.Length() - part_len
rawSeqA = seqA.Sequence()[startA:]
qualSeqA = seqA.Qualities()[startA:]
partLen = len(rawSeqA)
rawSeqB = seqB.Sequence()[0:partLen]
qualSeqB = seqB.Qualities()[0:partLen]
extra3 = seqB.Length() - partLen
score = _FillMatrixPeLeftAlign(
raw_seqA, qual_seqA, raw_seqB, qual_seqB, gap,
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
&arena.pointer.scoreMatrix,
&arena.pointer.pathMatrix)
} else {
@@ -319,20 +319,20 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
startB = 0
}
extra5 = startB
raw_seqB = seqB.Sequence()[startB:]
qual_seqB = seqB.Qualities()[startB:]
part_len = len(raw_seqB)
raw_seqA = seqA.Sequence()[:part_len]
qual_seqA = seqA.Qualities()[:part_len]
extra3 = part_len - seqA.Length()
rawSeqB = seqB.Sequence()[startB:]
qualSeqB = seqB.Qualities()[startB:]
partLen = len(rawSeqB)
rawSeqA = seqA.Sequence()[:partLen]
qualSeqA = seqA.Qualities()[:partLen]
extra3 = partLen - seqA.Length()
score = _FillMatrixPeRightAlign(
raw_seqA, qual_seqA, raw_seqB, qual_seqB, gap,
rawSeqA, qualSeqA, rawSeqB, qualSeqB, gap,
&arena.pointer.scoreMatrix,
&arena.pointer.pathMatrix)
}
arena.pointer.path = _Backtracking(arena.pointer.pathMatrix,
len(raw_seqA), len(raw_seqB),
len(rawSeqA), len(rawSeqB),
&arena.pointer.path)
} else {
@@ -340,27 +340,27 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
startA = shift
startB = 0
extra5 = -startA
qual_seqA = seqA.Qualities()[startA:]
part_len = len(qual_seqA)
qual_seqB = seqB.Qualities()[0:part_len]
extra3 = seqB.Length() - part_len
qualSeqA = seqA.Qualities()[startA:]
partLen = len(qualSeqA)
qualSeqB = seqB.Qualities()[0:partLen]
extra3 = seqB.Length() - partLen
score = 0
} else {
startA = 0
startB = -shift
extra5 = startB
qual_seqB = seqB.Qualities()[startB:]
part_len = len(qual_seqB)
extra3 = part_len - seqA.Length()
qual_seqA = seqA.Qualities()[:part_len]
qualSeqB = seqB.Qualities()[startB:]
partLen = len(qualSeqB)
extra3 = partLen - seqA.Length()
qualSeqA = seqA.Qualities()[:partLen]
}
score = 0
for i, qualA := range qual_seqA {
qualB := qual_seqB[i]
for i, qualA := range qualSeqA {
qualB := qualSeqB[i]
score += _NucScorePartMatchMatch[qualA][qualB]
}
arena.pointer.path = arena.pointer.path[:0]
arena.pointer.path = append(arena.pointer.path, 0, part_len)
arena.pointer.path = append(arena.pointer.path, 0, partLen)
}
arena.pointer.path[0] += extra5