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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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4
pkg/obiformats/csv_read.go
View File

@@ -7,8 +7,8 @@ import (
"path"
"strings"
"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"
"github.com/goccy/go-json"
@@ -143,7 +143,7 @@ func ReadCSV(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, err
go _ParseCsvFile(opt.Source(),
reader,
out,
byte(obioptions.InputQualityShift()),
obidefault.ReadQualitiesShift(),
opt.BatchSize())
go func() {

4
pkg/obiformats/csv_writer.go
View File

@@ -3,7 +3,7 @@ package obiformats
import (
"fmt"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
@@ -54,7 +54,7 @@ func CSVSequenceRecord(sequence *obiseq.BioSequence, opt Options) []string {
l := sequence.Len()
q := sequence.Qualities()
ascii := make([]byte, l)
quality_shift := obioptions.OutputQualityShift()
quality_shift := obidefault.WriteQualitiesShift()
for j := 0; j < l; j++ {
ascii[j] = uint8(q[j]) + uint8(quality_shift)
}

4
pkg/obiformats/fastqseq_read.go
View File

@@ -7,8 +7,8 @@ import (
"os"
"path"
"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"
log "github.com/sirupsen/logrus"
@@ -341,7 +341,7 @@ func ReadFastq(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, e
go _ParseFastqFile(
chkchan,
out,
byte(obioptions.InputQualityShift()),
obidefault.ReadQualitiesShift(),
opt.ReadQualities(),
)
}

6
pkg/obiformats/fastseq_read.go
View File

@@ -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())

6
pkg/obiformats/file_chunk_write.go
View File

@@ -3,7 +3,7 @@ package obiformats
import (
"io"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus"
)
@@ -12,7 +12,7 @@ func WriteFileChunk(
writer io.WriteCloser,
toBeClosed bool) ChannelFileChunk {
obiiter.RegisterAPipe()
obiutils.RegisterAPipe()
chunk_channel := make(ChannelFileChunk)
go func() {
@@ -53,7 +53,7 @@ func WriteFileChunk(
}
}
obiiter.UnregisterPipe()
obiutils.UnregisterPipe()
log.Debugf("The writer has been closed")
}()