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Patch rev complement and first implementation of --auto in obicsv

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Former-commit-id: f3020e81283b1073c4d1c2d2ff0887e3998e6764
This commit is contained in:
Eric Coissac
2023-11-07 09:37:07 +02:00
parent 6a6a6f6f2c
commit 61c30f9b6a
21 changed files with 270 additions and 107 deletions
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5
pkg/obiformats/fastseq_read.go
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@@ -15,6 +15,7 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
)
@@ -91,7 +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(opt.QualityShift()))
pointer := C.open_fast_sek_file(name, C.int32_t(obioptions.InputQualityShift()))
var err error
err = nil
@@ -150,7 +151,7 @@ func ReadFastSeqFromStdin(options ...WithOption) obiiter.IBioSequence {
}(newIter)
go _FastseqReader(opt.Source(),
C.open_fast_sek_stdin(C.int32_t(opt.QualityShift())),
C.open_fast_sek_stdin(C.int32_t(obioptions.InputQualityShift())),
newIter, opt.BatchSize())
log.Debugln("Full file batch mode : ", opt.FullFileBatch())