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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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7
pkg/obiformats/options.go
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@ -1,11 +1,12 @@
package obiformats
import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
type __options__ struct {
fastseq_header_parser obiseq.SeqAnnotator
fastseq_header_parser obiiter.SeqAnnotator
fastseq_header_writer func(*obiseq.BioSequence) string
with_progress_bar bool
buffer_size int
@ -58,7 +59,7 @@ func (opt Options) ParallelWorkers() int {
return opt.pointer.parallel_workers
}
func (opt Options) ParseFastSeqHeader() obiseq.SeqAnnotator {
func (opt Options) ParseFastSeqHeader() obiiter.SeqAnnotator {
return opt.pointer.fastseq_header_parser
}
@ -123,7 +124,7 @@ func OptionsQualitySolexa() WithOption {
return OptionsQualityShift(64)
}
func OptionsFastSeqHeaderParser(parser obiseq.SeqAnnotator) WithOption {
func OptionsFastSeqHeaderParser(parser obiiter.SeqAnnotator) WithOption {
f := WithOption(func(opt Options) {
opt.pointer.fastseq_header_parser = parser
})