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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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11
pkg/obichunk/chunk_on_disk.go
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@ -8,6 +8,7 @@ import (
"path/filepath"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
@ -33,12 +34,12 @@ func find(root, ext string) []string {
return a
}
func ISequenceChunkOnDisk(iterator obiseq.IBioSequenceBatch,
func ISequenceChunkOnDisk(iterator obiiter.IBioSequenceBatch,
classifier *obiseq.BioSequenceClassifier,
sizes ...int) (obiseq.IBioSequenceBatch, error) {
sizes ...int) (obiiter.IBioSequenceBatch, error) {
dir, err := tempDir()
if err != nil {
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
bufferSize := iterator.BufferSize()
@ -47,7 +48,7 @@ func ISequenceChunkOnDisk(iterator obiseq.IBioSequenceBatch,
bufferSize = sizes[0]
}
newIter := obiseq.MakeIBioSequenceBatch(bufferSize)
newIter := obiiter.MakeIBioSequenceBatch(bufferSize)
newIter.Add(1)
@ -86,7 +87,7 @@ func ISequenceChunkOnDisk(iterator obiseq.IBioSequenceBatch,
b.Recycle()
}
newIter.Push(obiseq.MakeBioSequenceBatch(order, chunck))
newIter.Push(obiiter.MakeBioSequenceBatch(order, chunck))
}