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Some code refactoring, a new version of obiuniq more efficient in memory and a first make file allowing to build obitools

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This commit is contained in:
Eric Coissac
2022-02-24 07:08:40 +01:00
parent 2e7c1834b0
commit eaf65fbcce
39 changed files with 1225 additions and 241 deletions
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13
pkg/obichunk/subchunks.go
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@ -5,6 +5,7 @@ import (
"sort"
"sync/atomic"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
@ -54,9 +55,9 @@ func (by _By) Sort(seqs []sSS) {
// End of the sort interface
//
func ISequenceSubChunk(iterator obiseq.IBioSequenceBatch,
func ISequenceSubChunk(iterator obiiter.IBioSequenceBatch,
classifier *obiseq.BioSequenceClassifier,
sizes ...int) (obiseq.IBioSequenceBatch, error) {
sizes ...int) (obiiter.IBioSequenceBatch, error) {
bufferSize := iterator.BufferSize()
nworkers := 4
@ -69,7 +70,7 @@ func ISequenceSubChunk(iterator obiseq.IBioSequenceBatch,
bufferSize = sizes[1]
}
newIter := obiseq.MakeIBioSequenceBatch(bufferSize)
newIter := obiiter.MakeIBioSequenceBatch(bufferSize)
newIter.Add(nworkers)
@ -86,7 +87,7 @@ func ISequenceSubChunk(iterator obiseq.IBioSequenceBatch,
return neworder
}
ff := func(iterator obiseq.IBioSequenceBatch,
ff := func(iterator obiiter.IBioSequenceBatch,
classifier *obiseq.BioSequenceClassifier) {
ordered := make([]sSS, 100)
@ -121,7 +122,7 @@ func ISequenceSubChunk(iterator obiseq.IBioSequenceBatch,
ss := obiseq.MakeBioSequenceSlice()
for i, v := range ordered {
if v.code != last {
newIter.Push(obiseq.MakeBioSequenceBatch(nextOrder(), ss))
newIter.Push(obiiter.MakeBioSequenceBatch(nextOrder(), ss))
ss = obiseq.MakeBioSequenceSlice()
last = v.code
}
@ -131,7 +132,7 @@ func ISequenceSubChunk(iterator obiseq.IBioSequenceBatch,
}
if len(ss) > 0 {
newIter.Push(obiseq.MakeBioSequenceBatch(nextOrder(), ss))
newIter.Push(obiiter.MakeBioSequenceBatch(nextOrder(), ss))
}
} else {
newIter.Push(batch.Reorder(nextOrder()))