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Reduce memory allocation events

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Former-commit-id: fbdb2afc857b02adc2593e2278d3bd838e99b0b2
This commit is contained in:
Eric Coissac
2024-06-22 21:01:53 +02:00
parent 54a138196c
commit e6b87ecd02
19 changed files with 166 additions and 75 deletions
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5
pkg/obitools/obiconvert/sequence_writer.go
View File

@@ -53,10 +53,7 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
opts = append(opts, obiformats.OptionsFastSeqHeaderFormat(obiformats.FormatFastSeqJsonHeader))
}
nworkers := obioptions.CLIParallelWorkers() / 4
if nworkers < 2 {
nworkers = 2
}
nworkers := obioptions.CLIWriteParallelWorkers()
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))

16
pkg/obitools/obipairing/pairing.go
View File

@@ -55,6 +55,8 @@ func JoinPairedSequence(seqA, seqB *obiseq.BioSequence, inplace bool) *obiseq.Bi
seqA = seqA.Copy()
}
seqA.Grow(seqB.Len() + 10)
seqA.WriteString("..........")
seqA.Write(seqB.Sequence())
@@ -108,13 +110,16 @@ func JoinPairedSequence(seqA, seqB *obiseq.BioSequence, inplace bool) *obiseq.Bi
func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
gap, scale float64, delta, minOverlap int, minIdentity float64, withStats bool,
inplace bool, fastAlign, fastModeRel bool,
arenaAlign obialign.PEAlignArena) *obiseq.BioSequence {
arenaAlign obialign.PEAlignArena, shifh_buff *map[int]int) *obiseq.BioSequence {
score, path, fastcount, over, fastscore := obialign.PEAlign(seqA, seqB,
score, path, fastcount, over, fastscore := obialign.PEAlign(
seqA, seqB,
gap, scale,
fastAlign, delta, fastModeRel,
arenaAlign)
cons, match := obialign.BuildQualityConsensus(seqA, seqB, path, true)
arenaAlign, shifh_buff,
)
cons, match := obialign.BuildQualityConsensus(seqA, seqB, path, true, arenaAlign)
left := path[0]
right := 0
@@ -238,6 +243,7 @@ func IAssemblePESequencesBatch(iterator obiiter.IBioSequence,
f := func(iterator obiiter.IBioSequence, wid int) {
arena := obialign.MakePEAlignArena(150, 150)
shifts := make(map[int]int)
for iterator.Next() {
batch := iterator.Get()
@@ -246,7 +252,7 @@ func IAssemblePESequencesBatch(iterator obiiter.IBioSequence,
B := A.PairedWith()
cons[i] = AssemblePESequences(A, B.ReverseComplement(true),
gap, scale,
delta, minOverlap, minIdentity, withStats, true, fastAlign, fastModeRel, arena)
delta, minOverlap, minIdentity, withStats, true, fastAlign, fastModeRel, arena, &shifts)
}
newIter.Push(obiiter.MakeBioSequenceBatch(
batch.Order(),

3
pkg/obitools/obitagpcr/pcrtag.go
View File

@@ -37,6 +37,7 @@ func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
f := func(iterator obiiter.IBioSequence, wid int) {
arena := obialign.MakePEAlignArena(150, 150)
var err error
shifts := make(map[int]int)
for iterator.Next() {
batch := iterator.Get()
@@ -46,7 +47,7 @@ func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
A.Copy(), B.ReverseComplement(false),
gap, scale,
delta, minOverlap, minIdentity, withStats, true,
fastAlign, fastScoreRel, arena,
fastAlign, fastScoreRel, arena, &shifts,
)
consensus, err = ngsfilter.ExtractBarcode(consensus, true)