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Merge obiminion and obiconsensus

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Former-commit-id: 49d65d671e9fe4454de60c20507c3d8df6e9c51c
This commit is contained in:
Eric Coissac
2024-05-14 17:53:32 +02:00
parent 7fcb0538a3
commit 61be8a55b1
7 changed files with 359 additions and 539 deletions
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6
cmd/obitools/obiconsensus/main.go
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@ -16,7 +16,6 @@ func main() {
optionParser := obioptions.GenerateOptionParser(obiconsensus.OptionSet)
_, args := optionParser(os.Args)
obiconvert.SetFullFileBatch()
fs, err := obiconvert.CLIReadBioSequences(args...)
@ -25,8 +24,9 @@ func main() {
os.Exit(1)
}
consensus := obiconsensus.Consensus(fs)
obiconvert.CLIWriteBioSequences(consensus, true)
cleaned := obiconsensus.CLIOBIMinion(fs)
obiconvert.CLIWriteBioSequences(cleaned, true)
obiiter.WaitForLastPipe()

33
cmd/obitools/obiminion/main.go
View File

@ -1,33 +0,0 @@
package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiminion"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
)
func main() {
optionParser := obioptions.GenerateOptionParser(obiminion.OptionSet)
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
cleaned := obiminion.CLIOBIMinion(fs)
obiconvert.CLIWriteBioSequences(cleaned, true)
obiiter.WaitForLastPipe()
}