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Change the memory management for thee BuildAlignment function

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This commit is contained in:
Eric Coissac
2022-01-15 19:10:16 +01:00
parent e8fff6477b
commit e1b7e1761c
11 changed files with 145 additions and 1329 deletions
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57
pkg/obitools/obipairing/pairing.go
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@@ -19,6 +19,13 @@ func _Abs(x int) int {
return x
}
// JoinPairedSequence paste two sequences putting 10 dots as separator.
// if both sequences havee quality scores a quality of 0 is assoociated
// to the added dot.
// If the inplace argument is set to 'true', memory allocated to the
// sequences provided are is used too limite reallocation. The two sequences
// provided as arguments can therefore not anymore used after the return of
// of the JoinPairedSequence. You have even noot to recycle them.
func JoinPairedSequence(seqA, seqB obiseq.BioSequence, inplace bool) obiseq.BioSequence {
if !inplace {
@@ -28,8 +35,14 @@ func JoinPairedSequence(seqA, seqB obiseq.BioSequence, inplace bool) obiseq.BioS
seqA.WriteString("..........")
seqA.Write(seqB.Sequence())
seqA.WriteQualities(obiseq.Quality{0, 0, 0, 0, 0, 0, 0, 0, 0, 0})
seqA.WriteQualities(seqB.Qualities())
if seqA.HasQualities() && seqB.HasQualities() {
seqA.WriteQualities(obiseq.Quality{0, 0, 0, 0, 0, 0, 0, 0, 0, 0})
seqA.WriteQualities(seqB.Qualities())
}
if inplace {
(&seqB).Recycle()
}
return seqA
}
@@ -38,21 +51,18 @@ func JoinPairedSequence(seqA, seqB obiseq.BioSequence, inplace bool) obiseq.BioS
// the obipairing strategy implemented in obialign.PEAlign using
// the gap and delta parametters.
// If the length of the overlap between both sequences is less than
// overlap_min, The alignment is substituted by a simple pasting
// overlapMin, The alignment is substituted by a simple pasting
// of the sequences with a strech of 10 dots in between them.
// the quality of the dots is set to 0.
// If the inplace parameter is set to true, the seqA and seqB are
// destroyed during the assembling process and cannot be reuse later on.
func AssemblePESequences(seqA, seqB obiseq.BioSequence,
gap, delta, overlap_min int, with_stats bool,
gap, delta, overlapMin int, withStats bool,
inplace bool,
arena_align obialign.PEAlignArena,
arena_cons obialign.BuildAlignArena,
arena_qual obialign.BuildAlignArena) obiseq.BioSequence {
arenaAlign obialign.PEAlignArena) obiseq.BioSequence {
score, path := obialign.PEAlign(seqA, seqB, gap, delta, arena_align)
cons, match := obialign.BuildQualityConsensus(seqA, seqB, path,
arena_cons, arena_qual)
score, path := obialign.PEAlign(seqA, seqB, gap, delta, arenaAlign)
cons, match := obialign.BuildQualityConsensus(seqA, seqB, path)
left := path[0]
right := 0
@@ -60,10 +70,10 @@ func AssemblePESequences(seqA, seqB obiseq.BioSequence,
right = path[len(path)-2]
}
lcons := cons.Length()
ali_length := lcons - _Abs(left) - _Abs(right)
aliLength := lcons - _Abs(left) - _Abs(right)
if ali_length >= overlap_min {
if with_stats {
if aliLength >= overlapMin {
if withStats {
annot := cons.Annotations()
annot["mode"] = "alignment"
annot["score"] = score
@@ -83,14 +93,14 @@ func AssemblePESequences(seqA, seqB obiseq.BioSequence,
annot["seq_b_single"] = right
}
score_norm := float64(0)
if ali_length > 0 {
score_norm = math.Round(float64(match)/float64(ali_length)*1000) / 1000
scoreNorm := float64(0)
if aliLength > 0 {
scoreNorm = math.Round(float64(match)/float64(aliLength)*1000) / 1000
}
annot["ali_length"] = ali_length
annot["ali_length"] = aliLength
annot["seq_ab_match"] = match
annot["score_norm"] = score_norm
annot["score_norm"] = scoreNorm
if inplace {
(&seqA).Recycle()
@@ -100,21 +110,18 @@ func AssemblePESequences(seqA, seqB obiseq.BioSequence,
} else {
cons = JoinPairedSequence(seqA, seqB, inplace)
if with_stats {
if withStats {
annot := cons.Annotations()
annot["mode"] = "join"
}
if inplace {
(&seqB).Recycle()
}
}
return cons
}
func IAssemblePESequencesBatch(iterator obiseq.IPairedBioSequenceBatch,
gap, delta, overlap_min int, with_stats bool, sizes ...int) obiseq.IBioSequenceBatch {
gap, delta, overlapMin int, withStats bool, sizes ...int) obiseq.IBioSequenceBatch {
nworkers := runtime.NumCPU() - 1
buffsize := iterator.BufferSize()
@@ -150,8 +157,6 @@ func IAssemblePESequencesBatch(iterator obiseq.IPairedBioSequenceBatch,
f := func(iterator obiseq.IPairedBioSequenceBatch, wid int) {
arena := obialign.MakePEAlignArena(150, 150)
barena1 := obialign.MakeBuildAlignArena(150, 150)
barena2 := obialign.MakeBuildAlignArena(150, 150)
// log.Printf("\n==> %d Wait data to align\n", wid)
// start := time.Now()
@@ -163,7 +168,7 @@ func IAssemblePESequencesBatch(iterator obiseq.IPairedBioSequenceBatch,
processed := 0
for i, A := range batch.Forward() {
B := batch.Reverse()[i]
cons[i] = AssemblePESequences(A, B, 2, 5, 20, true, true, arena, barena1, barena2)
cons[i] = AssemblePESequences(A, B, 2, 5, 20, true, true, arena)
if i%59 == 0 {
bar.Add(59)
processed += 59