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Refactoring of the default values

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This commit is contained in:
Eric Coissac
2025-01-24 18:09:59 +01:00
parent 3137c1f841
commit 9acb4a85a8
50 changed files with 337 additions and 166 deletions
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6
pkg/obiformats/fastseq_read.go
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@ -14,8 +14,8 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
@ -92,7 +92,7 @@ func ReadFastSeqFromFile(filename string, options ...WithOption) (obiiter.IBioSe
name := C.CString(filename)
defer C.free(unsafe.Pointer(name))
pointer := C.open_fast_sek_file(name, C.int32_t(obioptions.InputQualityShift()))
pointer := C.open_fast_sek_file(name, C.int32_t(obidefault.ReadQualitiesShift()))
var err error
err = nil
@ -151,7 +151,7 @@ func ReadFastSeqFromStdin(options ...WithOption) obiiter.IBioSequence {
}(newIter)
go _FastseqReader(opt.Source(),
C.open_fast_sek_stdin(C.int32_t(obioptions.InputQualityShift())),
C.open_fast_sek_stdin(C.int32_t(obidefault.ReadQualitiesShift())),
newIter, opt.BatchSize())
log.Debugln("Full file batch mode : ", opt.FullFileBatch())