Add a progress bar to chimera detection

cmd/obitools/obitag/main.go

@@ -73,10 +73,12 @@ func main() {
 
 	var identified obiiter.IBioSequence
 
+	fsrb := fs.Rebatch(obidefault.BatchSize())
+
 	if obitag.CLIGeometricMode() {
-		identified = obitag.CLIGeomAssignTaxonomy(fs, references, taxo)
+		identified = obitag.CLIGeomAssignTaxonomy(fsrb, references, taxo)
 	} else {
-		identified = obitag.CLIAssignTaxonomy(fs, references, taxo)
+		identified = obitag.CLIAssignTaxonomy(fsrb, references, taxo)
 	}
 
 	obiconvert.CLIWriteBioSequences(identified, true)

pkg/obioptions/version.go

@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "8448783"
+var _Commit = "8b379d3"
 var _Version = "Release 4.4.0"
 
 // Version returns the version of the obitools package.

pkg/obitools/obiclean/chimera.go

@@ -2,10 +2,12 @@ package obiclean
 
 import (
 	"fmt"
+	"os"
 	"sort"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
+	"github.com/schollz/progressbar/v3"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -119,8 +121,20 @@ func AnnotateChimera(samples map[string]*[]*seqPCR) {
 
 	}
 
+	pbopt := make([]progressbar.Option, 0, 5)
+	pbopt = append(pbopt,
+		progressbar.OptionSetWriter(os.Stderr),
+		progressbar.OptionSetWidth(15),
+		progressbar.OptionShowIts(),
+		progressbar.OptionSetPredictTime(true),
+		progressbar.OptionSetDescription("[Chimera detection]"),
+	)
+
+	bar := progressbar.NewOptions(len(samples), pbopt...)
+
 	for sn, sqs := range samples {
 		w(sn, sqs)
+		bar.Add(1)
 	}
 
 }

pkg/obitools/obiconvert/options.go

@@ -33,6 +33,7 @@ var __output_fastobi_format__ = false
 
 var __no_progress_bar__ = false
 var __skip_empty__ = false
+var __skip_on_error__ = false
 
 var __output_file_name__ = "-"
 var __paired_file_name__ = ""
@@ -97,6 +98,9 @@ func OutputOptionSet(options *getoptions.GetOpt) {
 	options.BoolVar(&__skip_empty__, "skip-empty", __skip_empty__,
 		options.Description("Sequences of length equal to zero are suppressed from the output"))
 
+	// options.BoolVar(&__skip_on_error__, "skip-on-error", __skip_on_error__,
+	// 	options.Description("Skip sequence with parsing error"))
+
 	options.BoolVar(&__output_in_fasta__, "fasta-output", false,
 		options.Description("Write sequence in fasta format (default if no quality data available)."))
 
@@ -172,6 +176,10 @@ func CLISkipEmpty() bool {
 	return __skip_empty__
 }
 
+func CLISkipOnError() bool {
+	return __skip_on_error__
+}
+
 func CLIInputFastHeaderFormat() string {
 	switch {
 	case __input_fastjson_format__: