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Takes into account the option parsing errors

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Former-commit-id: d0b3ed0b96a72f79f887df8fbc325427e63d7a73
This commit is contained in:
Eric Coissac
2023-03-07 11:06:08 +07:00
parent 6b52dc0700
commit 9811e440b8
15 changed files with 23 additions and 18 deletions
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2
cmd/obitools/obiannotate/main.go
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@ -32,7 +32,7 @@ func main() {
optionParser := obioptions.GenerateOptionParser(obiannotate.OptionSet)
_, args, _ := optionParser(os.Args)
_, args := optionParser(os.Args)
sequences, _ := obiconvert.CLIReadBioSequences(args...)
annotator := obiannotate.CLIAnnotationPipeline()

2
cmd/obitools/obiclean/main.go
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@ -13,7 +13,7 @@ import (
func main() {
optionParser := obioptions.GenerateOptionParser(obiclean.OptionSet)
_, args, _ := optionParser(os.Args)
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)

2
cmd/obitools/obicleandb/main.go
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@ -12,7 +12,7 @@ import (
func main() {
optionParser := obioptions.GenerateOptionParser(obicleandb.OptionSet)
_, args, _ := optionParser(os.Args)
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)

2
cmd/obitools/obicomplement/main.go
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@ -13,7 +13,7 @@ import (
func main() {
optionParser := obioptions.GenerateOptionParser(obiconvert.OptionSet)
_, args, _ := optionParser(os.Args)
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)

2
cmd/obitools/obiconvert/main.go
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@ -12,7 +12,7 @@ import (
func main() {
optionParser := obioptions.GenerateOptionParser(obiconvert.OptionSet)
_, args, _ := optionParser(os.Args)
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)
obiconvert.CLIWriteBioSequences(fs, true)

2
cmd/obitools/obicount/main.go
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@ -31,7 +31,7 @@ func main() {
obicount.OptionSet,
)
_, args, _ := optionParser(os.Args)
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)
nvariant, nread, nsymbol := fs.Count(true)

13
cmd/obitools/obicsv/main.go
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@ -1,16 +1,21 @@
package main
import (
"os"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obicsv"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
)
func main() {
// optionParser := obioptions.GenerateOptionParser(obiconvert.OptionSet)
optionParser := obioptions.GenerateOptionParser(obicsv.OptionSet)
// _, args, _ := optionParser(os.Args)
_, args := optionParser(os.Args)
// fs, _ := obiconvert.ReadBioSequences(args...)
// //obicsv.CLIWriteCSV(fs, true)
fs, _ := obiconvert.CLIReadBioSequences(args...)
obicsv.CLIWriteCSV(fs, true)
obiiter.WaitForLastPipe()

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

@ -13,7 +13,7 @@ import (
func main() {
optionParser := obioptions.GenerateOptionParser(obidistribute.OptionSet)
_, args, _ := optionParser(os.Args)
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)

2
cmd/obitools/obifind/main.go
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@ -11,7 +11,7 @@ import (
func main() {
optionParser := obioptions.GenerateOptionParser(obifind.OptionSet)
_, args, _ := optionParser(os.Args)
_, args := optionParser(os.Args)
//prof, _ := os.Create("obifind.prof")
//pprof.StartCPUProfile(prof)

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

@ -32,7 +32,7 @@ func main() {
optionParser := obioptions.GenerateOptionParser(obigrep.OptionSet)
_, args, _ := optionParser(os.Args)
_, args := optionParser(os.Args)
sequences, _ := obiconvert.CLIReadBioSequences(args...)
selected := obigrep.CLIFilterSequence(sequences)

2
cmd/obitools/obimultiplex/main.go
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@ -27,7 +27,7 @@ func main() {
optionParser := obioptions.GenerateOptionParser(obimultiplex.OptionSet)
_, args, _ := optionParser(os.Args)
_, args := optionParser(os.Args)
sequences, _ := obiconvert.CLIReadBioSequences(args...)
amplicons, _ := obimultiplex.IExtractBarcode(sequences)

2
cmd/obitools/obipcr/main.go
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@ -29,7 +29,7 @@ func main() {
optionParser := obioptions.GenerateOptionParser(obipcr.OptionSet)
_, args, _ := optionParser(os.Args)
_, args := optionParser(os.Args)
sequences, _ := obiconvert.CLIReadBioSequences(args...)
amplicons, _ := obipcr.PCR(sequences)

2
cmd/obitools/obirefidx/main.go
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@ -13,7 +13,7 @@ import (
func main() {
optionParser := obioptions.GenerateOptionParser(obirefidx.OptionSet)
_, args, _ := optionParser(os.Args)
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)
indexed := obirefidx.IndexReferenceDB(fs)

2
cmd/obitools/obitag/main.go
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@ -31,7 +31,7 @@ func main() {
optionParser := obioptions.GenerateOptionParser(obitag.OptionSet)
_, args, _ := optionParser(os.Args)
_, args := optionParser(os.Args)
fs, _ := obiconvert.CLIReadBioSequences(args...)
identified := obitag.AssignTaxonomy(fs)

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

@ -32,7 +32,7 @@ func main() {
optionParser := obioptions.GenerateOptionParser(obiuniq.OptionSet)
_, args, _ := optionParser(os.Args)
_, args := optionParser(os.Args)
sequences, _ := obiconvert.CLIReadBioSequences(args...)
unique := obiuniq.Unique(sequences)