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trial on rewriting obimultiplex

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Former-commit-id: d00f3353d83760dc878c6411ad344d96216096a7
This commit is contained in:
Eric Coissac
2024-06-04 16:50:07 +02:00
parent 65f5109957
commit a0a9fb461c
1 changed files with 56 additions and 0 deletions
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56
cmd/obitools/obimultiplex2/main.go Normal file
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package main
import (
"fmt"
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"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/obimultiplex2"
)
func main() {
// f, err := os.Create("cpu.pprof")
// if err != nil {
// log.Fatal(err)
// }
// pprof.StartCPUProfile(f)
// defer pprof.StopCPUProfile()
// ftrace, err := os.Create("cpu.trace")
// if err != nil {
// log.Fatal(err)
// }
// trace.Start(ftrace)
// defer trace.Stop()
optionParser := obioptions.GenerateOptionParser(obimultiplex2.OptionSet)
_, args := optionParser(os.Args)
if obimultiplex2.CLIAskConfigTemplate() {
fmt.Print(obimultiplex2.CLIConfigTemplate())
os.Exit(0)
}
if !obimultiplex2.CLIHasNGSFilterFile() {
log.Error("You must provide a tag list file following the NGSFilter format")
os.Exit(1)
}
sequences, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
amplicons, _ := obimultiplex2.IExtractBarcode(sequences)
obiconvert.CLIWriteBioSequences(amplicons, true)
amplicons.Wait()
obiiter.WaitForLastPipe()
}