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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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9
pkg/obichunk/chunks.go
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@ -4,12 +4,13 @@ import (
"log"
"sync"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func ISequenceChunk(iterator obiseq.IBioSequenceBatch,
func ISequenceChunk(iterator obiiter.IBioSequenceBatch,
classifier *obiseq.BioSequenceClassifier,
sizes ...int) (obiseq.IBioSequenceBatch, error) {
sizes ...int) (obiiter.IBioSequenceBatch, error) {
bufferSize := iterator.BufferSize()
@ -17,7 +18,7 @@ func ISequenceChunk(iterator obiseq.IBioSequenceBatch,
bufferSize = sizes[0]
}
newIter := obiseq.MakeIBioSequenceBatch(bufferSize)
newIter := obiiter.MakeIBioSequenceBatch(bufferSize)
newIter.Add(1)
@ -64,7 +65,7 @@ func ISequenceChunk(iterator obiseq.IBioSequenceBatch,
for _, chunck := range chunks {
if len(*chunck) > 0 {
newIter.Push(obiseq.MakeBioSequenceBatch(order, *chunck))
newIter.Push(obiiter.MakeBioSequenceBatch(order, *chunck))
order++
}