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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/obiformats/fastseq_header.go
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@ -3,6 +3,7 @@ package obiformats
import (
"strings"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
@ -14,14 +15,16 @@ func ParseGuessedFastSeqHeader(sequence *obiseq.BioSequence) {
}
}
func IParseFastSeqHeaderBatch(iterator obiseq.IBioSequenceBatch, options ...WithOption) obiseq.IBioSequenceBatch {
func IParseFastSeqHeaderBatch(iterator obiiter.IBioSequenceBatch,
options ...WithOption) obiiter.IBioSequenceBatch {
opt := MakeOptions(options)
return iterator.MakeIWorker(obiseq.AnnotatorToSeqWorker(opt.ParseFastSeqHeader()),
return iterator.MakeIWorker(obiiter.AnnotatorToSeqWorker(opt.ParseFastSeqHeader()),
opt.ParallelWorkers(),
opt.BufferSize())
}
func IParseFastSeqHeader(iterator obiseq.IBioSequence, options ...WithOption) obiseq.IBioSequence {
func IParseFastSeqHeader(iterator obiiter.IBioSequence,
options ...WithOption) obiiter.IBioSequence {
opt := MakeOptions(options)
return IParseFastSeqHeaderBatch(iterator.IBioSequenceBatch(opt.BatchSize(),