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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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3
pkg/obitools/obiconvert/sequence_reader.go
View File

@@ -9,6 +9,7 @@ import (
"github.com/goombaio/orderedset"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
@@ -99,7 +100,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
opts = append(opts, obiformats.OptionsFastSeqHeaderParser(obiformats.ParseGuessedFastSeqHeader))
}
opts = append(opts, obiformats.OptionsReadQualities(obioptions.CLIReadQualities()))
opts = append(opts, obiformats.OptionsReadQualities(obidefault.ReadQualities()))
nworkers := obioptions.CLIReadParallelWorkers()
if nworkers < 2 {

6
pkg/obitools/obicsv/iter.go
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@@ -7,7 +7,7 @@ import (
"sync/atomic"
"time"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"github.com/tevino/abool/v2"
log "github.com/sirupsen/logrus"
@@ -57,7 +57,7 @@ func NewICSVRecord() *ICSVRecord {
lock := sync.RWMutex{}
i.lock = &lock
obiiter.RegisterAPipe()
obiutils.RegisterAPipe()
return &i
}
@@ -275,7 +275,7 @@ func (iterator *ICSVRecord) Push(batch CSVRecordBatch) {
func (iterator *ICSVRecord) Close() {
close(iterator.channel)
obiiter.UnregisterPipe()
obiutils.UnregisterPipe()
}
func (iterator *ICSVRecord) WaitAndClose() {

4
pkg/obitools/obicsv/sequence.go
View File

@@ -4,8 +4,8 @@ import (
"log"
"slices"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
)
func CSVSequenceHeader(opt Options) CSVHeader {
@@ -95,7 +95,7 @@ func CSVBatchFromSequences(batch obiiter.BioSequenceBatch, opt Options) CSVRecor
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)
}

2
pkg/obitools/obimatrix/obimatrix.go
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@@ -122,7 +122,7 @@ func IMatrix(iterator obiiter.IBioSequence) *MatrixData {
}
waiter.Wait()
obiiter.WaitForLastPipe()
obiutils.WaitForLastPipe()
rep := summaries[0]

2
pkg/obitools/obisummary/obisummary.go
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@@ -187,7 +187,7 @@ func ISummary(iterator obiiter.IBioSequence, summarise []string) map[string]inte
}
waiter.Wait()
obiiter.WaitForLastPipe()
obiutils.WaitForLastPipe()
rep := summaries[0]

3
pkg/obitools/obitag/options.go
View File

@@ -8,6 +8,7 @@ import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"github.com/DavidGamba/go-getoptions"
)
@@ -112,7 +113,7 @@ func CLISaveRefetenceDB(db obiseq.BioSequenceSlice) {
}
newIter.Recycle()
obiiter.WaitForLastPipe()
obiutils.WaitForLastPipe()
}
}