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A global version of a Slice pool

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This commit is contained in:
Eric Coissac
2022-01-16 00:21:42 +01:00
parent e1b7e1761c
commit 576a9f4d2d
11 changed files with 227 additions and 149 deletions
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54
pkg/obialign/alignment.go
View File

@ -68,22 +68,22 @@ 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 := _BuildAlignArenaPool.Get().(*[]byte)
defer _BuildAlignArenaPool.Put(bufferSA)
bufferSA := obiseq.GetSlice()
defer obiseq.RecycleSlice(bufferSA)
bufferSB := _BuildAlignArenaPool.Get().(*[]byte)
defer _BuildAlignArenaPool.Put(bufferSB)
bufferSB := obiseq.GetSlice()
defer obiseq.RecycleSlice(bufferSB)
_BuildAlignment(seqA.Sequence(), seqB.Sequence(), path, gap,
bufferSA,
bufferSB)
&bufferSA,
&bufferSB)
seqA = obiseq.MakeBioSequence(seqA.Id(),
*bufferSA,
bufferSA,
seqA.Definition())
seqB = obiseq.MakeBioSequence(seqB.Id(),
*bufferSB,
bufferSB,
seqB.Definition())
return seqA, seqB
@ -112,27 +112,23 @@ func BuildAlignment(seqA, seqB obiseq.BioSequence,
// return.
func BuildQualityConsensus(seqA, seqB obiseq.BioSequence, path []int) (obiseq.BioSequence, int) {
bufferSA := _BuildAlignArenaPool.Get().(*[]byte)
defer _BuildAlignArenaPool.Put(bufferSA)
bufferSA := obiseq.GetSlice()
bufferSB := obiseq.GetSlice()
defer obiseq.RecycleSlice(bufferSB)
bufferSB := _BuildAlignArenaPool.Get().(*[]byte)
defer _BuildAlignArenaPool.Put(bufferSB)
bufferQA := _BuildAlignArenaPool.Get().(*[]byte)
defer _BuildAlignArenaPool.Put(bufferQA)
bufferQB := _BuildAlignArenaPool.Get().(*[]byte)
defer _BuildAlignArenaPool.Put(bufferQB)
bufferQA := obiseq.GetSlice()
bufferQB := obiseq.GetSlice()
defer obiseq.RecycleSlice(bufferQB)
_BuildAlignment(seqA.Sequence(), seqB.Sequence(), path, ' ',
bufferSA, bufferSB)
&bufferSA, &bufferSB)
// log.Printf("#1 %s--> la : %d,%p lb : %d,%p qa : %d,%p qb : %d,%p\n", stamp,
// len(*bufferSA), bufferSA, len(*bufferSB), bufferSB,
// len(*bufferQA), bufferQA, len(*bufferQB), bufferQB)
_BuildAlignment(seqA.Qualities(), seqB.Qualities(), path, byte(0),
bufferQA, bufferQB)
&bufferQA, &bufferQB)
// log.Printf("#2 %s--> la : %d,%p lb : %d,%p qa : %d,%p qb : %d,%p\n", stamp,
// len(*bufferSA), bufferSA, len(*bufferSB), bufferSB,
@ -145,23 +141,23 @@ func BuildQualityConsensus(seqA, seqB obiseq.BioSequence, path []int) (obiseq.Bi
match := 0
for i, qA = range *bufferQA {
nA := (*bufferSA)[i]
nB := (*bufferSB)[i]
qB = (*bufferQB)[i]
for i, qA = range bufferQA {
nA := bufferSA[i]
nB := bufferSB[i]
qB = bufferQB[i]
if qA > qB {
qM = qA
qm = qB
}
if qB > qA {
(*bufferSA)[i] = (*bufferSB)[i]
bufferSA[i] = bufferSB[i]
qM = qB
qm = qA
}
if qB == qA && nA != nB {
nuc := _FourBitsBaseCode[nA&31] | _FourBitsBaseCode[nB&31]
(*bufferSA)[i] = _FourBitsBaseDecode[nuc]
bufferSA[i] = _FourBitsBaseDecode[nuc]
}
q := qA + qB
@ -179,15 +175,15 @@ func BuildQualityConsensus(seqA, seqB obiseq.BioSequence, path []int) (obiseq.Bi
q = 90
}
(*bufferQA)[i] = q
bufferQA[i] = q
}
consSeq := obiseq.MakeBioSequence(
seqA.Id(),
(*bufferSA),
bufferSA,
seqA.Definition(),
)
consSeq.SetSequence((*bufferQA))
consSeq.SetQualities(bufferQA)
return consSeq, match
}

11
pkg/obialign/pairedendalign.go
View File

@ -281,11 +281,6 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
_InitDNAScoreMatrix()
}
// log.Println("==============")
// log.Println(seqA.String())
// log.Println(seqB.String())
// log.Println("--------------")
index := obikmer.Index4mer(seqA,
&arena.pointer.fastIndex,
&arena.pointer.fastBuffer)
@ -303,6 +298,9 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
// 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
if shift > 0 {
startA = shift - delta
if startA < 0 {
@ -321,6 +319,9 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
&arena.pointer.scoreMatrix,
&arena.pointer.pathMatrix)
} else {
// Both overlaping regions are identicals
startA = 0
startB = -shift - delta
if startB < 0 {