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introduce obidefault

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This commit is contained in:
Eric Coissac
2025-01-27 17:12:45 +01:00
parent 0a567f621c
commit 7c4042df6b
69 changed files with 505 additions and 479 deletions
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3
cmd/obitools/obicleandb/main.go
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@ -3,6 +3,7 @@ package main
import (
"os"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicleandb"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@ -11,7 +12,7 @@ import (
)
func main() {
obioptions.SetBatchSize(10)
obidefault.SetBatchSize(10)
optionParser := obioptions.GenerateOptionParser(obicleandb.OptionSet)

5
cmd/obitools/obiconvert/main.go
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@ -3,6 +3,7 @@ package main
import (
"os"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@ -10,8 +11,8 @@ import (
)
func main() {
obioptions.SetStrictReadWorker(2)
obioptions.SetStrictWriteWorker(2)
obidefault.SetStrictReadWorker(2)
obidefault.SetStrictWriteWorker(2)
optionParser := obioptions.GenerateOptionParser(obiconvert.OptionSet)

3
cmd/obitools/obicount/main.go
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@ -4,6 +4,7 @@ import (
"fmt"
"os"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obicount"
@ -33,7 +34,7 @@ func main() {
_, args := optionParser(os.Args)
obioptions.SetStrictReadWorker(min(4, obioptions.CLIParallelWorkers()))
obidefault.SetStrictReadWorker(min(4, obidefault.ParallelWorkers()))
fs, err := obiconvert.CLIReadBioSequences(args...)
obiconvert.OpenSequenceDataErrorMessage(args, err)

5
cmd/obitools/obidemerge/main.go
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@ -3,6 +3,7 @@ package main
import (
"os"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obidemerge"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@ -11,8 +12,8 @@ import (
)
func main() {
obioptions.SetStrictReadWorker(2)
obioptions.SetStrictWriteWorker(2)
obidefault.SetStrictReadWorker(2)
obidefault.SetStrictWriteWorker(2)
optionParser := obioptions.GenerateOptionParser(obidemerge.OptionSet)

5
cmd/obitools/obijoin/main.go
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@ -3,6 +3,7 @@ package main
import (
"os"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obijoin"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@ -11,8 +12,8 @@ import (
)
func main() {
obioptions.SetStrictReadWorker(2)
obioptions.SetStrictWriteWorker(2)
obidefault.SetStrictReadWorker(2)
obidefault.SetStrictWriteWorker(2)
optionParser := obioptions.GenerateOptionParser(obijoin.OptionSet)

7
cmd/obitools/obipairing/main.go
View File

@ -5,6 +5,7 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obipairing"
@ -33,8 +34,8 @@ func main() {
optionParser(os.Args)
obioptions.SetStrictReadWorker(2)
obioptions.SetStrictWriteWorker(2)
obidefault.SetStrictReadWorker(2)
obidefault.SetStrictWriteWorker(2)
pairs, err := obipairing.CLIPairedSequence()
if err != nil {
@ -51,7 +52,7 @@ func main() {
obipairing.CLIFastMode(),
obipairing.CLIFastRelativeScore(),
obipairing.CLIWithStats(),
obioptions.CLIParallelWorkers(),
obidefault.ParallelWorkers(),
)
obiconvert.CLIWriteBioSequences(paired, true)

9
cmd/obitools/obipcr/main.go
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@ -3,6 +3,7 @@ package main
import (
"os"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obipcr"
@ -23,10 +24,10 @@ func main() {
// trace.Start(ftrace)
// defer trace.Stop()
obioptions.SetWorkerPerCore(2)
obioptions.SetReadWorkerPerCore(0.5)
obioptions.SetParallelFilesRead(obioptions.CLIParallelWorkers() / 4)
obioptions.SetBatchSize(10)
obidefault.SetWorkerPerCore(2)
obidefault.SetReadWorkerPerCore(0.5)
obidefault.SetParallelFilesRead(obidefault.ParallelWorkers() / 4)
obidefault.SetBatchSize(10)
optionParser := obioptions.GenerateOptionParser(obipcr.OptionSet)

9
cmd/obitools/obitag/main.go
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@ -6,6 +6,7 @@ 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/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
@ -33,10 +34,10 @@ func main() {
// trace.Start(ftrace)
// defer trace.Stop()
obioptions.SetWorkerPerCore(2)
obioptions.SetStrictReadWorker(1)
obioptions.SetStrictWriteWorker(1)
obioptions.SetBatchSize(10)
obidefault.SetWorkerPerCore(2)
obidefault.SetStrictReadWorker(1)
obidefault.SetStrictWriteWorker(1)
obidefault.SetBatchSize(10)
optionParser := obioptions.GenerateOptionParser(obitag.OptionSet)

3
cmd/obitools/obitagpcr/main.go
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@ -5,6 +5,7 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obipairing"
@ -30,7 +31,7 @@ func main() {
// trace.Start(ftrace)
// defer trace.Stop()
obioptions.SetWorkerPerCore(1)
obidefault.SetWorkerPerCore(1)
optionParser := obioptions.GenerateOptionParser(obitagpcr.OptionSet)

2
cmd/obitools/obiuniq/main.go
View File

@ -31,7 +31,7 @@ func main() {
// trace.Start(ftrace)
// defer trace.Stop()
obioptions.SetBatchSize(10)
obidefault.SetBatchSize(10)
obidefault.SetReadQualities(false)
optionParser := obioptions.GenerateOptionParser(obiuniq.OptionSet)

4
cmd/test/main.go
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@ -3,13 +3,13 @@ package main
import (
"os"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitaxformat"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
func main() {
obitaxformat.DetectTaxonomyFormat(os.Args[1])
obitax.DetectTaxonomyFormat(os.Args[1])
println(obiutils.RemoveAllExt("toto/tutu/test.txt"))
println(obiutils.Basename("toto/tutu/test.txt"))