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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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21
pkg/obichunk/unique.go
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@ -3,26 +3,27 @@ package obichunk
import (
"sync"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func IUniqueSequence(iterator obiseq.IBioSequenceBatch,
options ...WithOption) (obiseq.IBioSequenceBatch, error) {
func IUniqueSequence(iterator obiiter.IBioSequenceBatch,
options ...WithOption) (obiiter.IBioSequenceBatch, error) {
var err error
opts := MakeOptions(options)
nworkers := opts.ParallelWorkers()
iUnique := obiseq.MakeIBioSequenceBatch(opts.BufferSize())
iUnique := obiiter.MakeIBioSequenceBatch(opts.BufferSize())
if opts.SortOnDisk() {
nworkers = 1
iterator, err = ISequenceChunkOnDisk(iterator,
obiseq.HashClassifier(opts.BatchCount()),
opts.BufferSize())
0)
if err != nil {
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
} else {
@ -31,7 +32,7 @@ func IUniqueSequence(iterator obiseq.IBioSequenceBatch,
opts.BufferSize())
if err != nil {
return obiseq.NilIBioSequenceBatch, err
return obiiter.NilIBioSequenceBatch, err
}
}
@ -53,12 +54,12 @@ func IUniqueSequence(iterator obiseq.IBioSequenceBatch,
return neworder
}
var ff func(obiseq.IBioSequenceBatch, *obiseq.BioSequenceClassifier, int)
var ff func(obiiter.IBioSequenceBatch, *obiseq.BioSequenceClassifier, int)
cat := opts.Categories()
na := opts.NAValue()
ff = func(input obiseq.IBioSequenceBatch,
ff = func(input obiiter.IBioSequenceBatch,
classifier *obiseq.BioSequenceClassifier,
icat int) {
icat--
@ -67,9 +68,9 @@ func IUniqueSequence(iterator obiseq.IBioSequenceBatch,
1,
opts.BufferSize())
var next obiseq.IBioSequenceBatch
var next obiiter.IBioSequenceBatch
if icat >= 0 {
next = obiseq.MakeIBioSequenceBatch(opts.BufferSize())
next = obiiter.MakeIBioSequenceBatch(opts.BufferSize())
iUnique.Add(1)
go ff(next,