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Patch a bug on writing to stdout, and add clearer error on openning data files

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This commit is contained in:
Eric Coissac
2024-08-13 09:45:28 +02:00
parent bdb96dda94
commit 31bfc88eb9
43 changed files with 1654 additions and 696 deletions
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7
cmd/obitools/obirefidx/main.go
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@@ -3,8 +3,6 @@ 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/obirefidx"
@@ -18,11 +16,8 @@ func main() {
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
obiconvert.OpenSequenceDataErrorMessage(args, err)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
indexed := obirefidx.IndexReferenceDB(fs)
obiconvert.CLIWriteBioSequences(indexed, true)