Start to use leveled log

cmd/obitools/obicount/main.go

@@ -34,7 +34,7 @@ func main() {
 	_, args, _ := optionParser(os.Args)
 
 	fs, _ := obiconvert.ReadBioSequencesBatch(args...)
-	nread, nvariant, nsymbol := fs.Count(true)
+	nvariant, nread, nsymbol := fs.Count(true)
 
 	if obicount.CLIIsPrintingVariantCount() {
 		fmt.Printf(" %d", nvariant)

cmd/obitools/obimultiplex/main.go

@@ -1,7 +1,7 @@
 package main
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 	"os"
 	"runtime/pprof"
 

cmd/obitools/obipairing/main.go

@@ -1,7 +1,7 @@
 package main
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 	"os"
 	"runtime/trace"
 

cmd/obitools/obipcr/main.go

@@ -1,7 +1,7 @@
 package main
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 	"os"
 	"runtime/trace"
 

cmd/obitools/obiuniq/main.go

@@ -1,7 +1,7 @@
 package main
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 	"os"
 	"runtime/pprof"
 

pkg/obialign/pairedendalign.go

@@ -1,7 +1,7 @@
 package obialign
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obikmer"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"

pkg/obiapat/pcr.go

@@ -1,7 +1,7 @@
 package obiapat
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"

pkg/obichunk/chunk_on_disk.go

@@ -3,10 +3,11 @@ package obichunk
 import (
 	"io/fs"
 	"io/ioutil"
-	"log"
 	"os"
 	"path/filepath"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
@@ -55,7 +56,7 @@ func ISequenceChunkOnDisk(iterator obiiter.IBioSequenceBatch,
 	go func() {
 		defer func() {
 			os.RemoveAll(dir)
-			log.Println("Clear the cache directory")
+			log.Debugln("Clear the cache directory")
 		}()
 
 		newIter.Wait()
@@ -68,7 +69,8 @@ func ISequenceChunkOnDisk(iterator obiiter.IBioSequenceBatch,
 	)
 
 	fileNames := find(dir, ".fastx")
-	log.Println("batch count ", len(fileNames))
+	nbatch := len(fileNames)
+	log.Infof("Data splitted over %d batches", nbatch)
 
 	go func() {
 
@@ -88,6 +90,8 @@ func ISequenceChunkOnDisk(iterator obiiter.IBioSequenceBatch,
 			}
 
 			newIter.Push(obiiter.MakeBioSequenceBatch(order, chunck))
+			log.Infof("Start processing of batch %d/%d : %d sequences",
+				order, nbatch, len(chunck))
 
 		}
 

pkg/obichunk/chunks.go

@@ -1,7 +1,7 @@
 package obichunk
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 	"sync"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"

pkg/obichunk/options.go

@@ -9,6 +9,7 @@ type __options__ struct {
 	bufferSize      int
 	batchSize       int
 	parallelWorkers int
+	noSingleton     bool
 }
 
 type Options struct {
@@ -27,6 +28,7 @@ func MakeOptions(setters []WithOption) Options {
 		bufferSize:      2,
 		batchSize:       5000,
 		parallelWorkers: 4,
+		noSingleton:     false,
 	}
 
 	opt := Options{&o}
@@ -79,6 +81,10 @@ func (opt Options) SortOnDisk() bool {
 	return opt.pointer.cacheOnDisk
 }
 
+func (opt Options) NoSingleton() bool {
+	return opt.pointer.noSingleton
+}
+
 func OptionSortOnDisk() WithOption {
 	f := WithOption(func(opt Options) {
 		opt.pointer.cacheOnDisk = true
@@ -149,3 +155,19 @@ func OptionsBufferSize(size int) WithOption {
 
 	return f
 }
+
+func OptionsNoSingleton() WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.noSingleton = true
+	})
+
+	return f
+}
+
+func OptionsWithSingleton() WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.noSingleton = false
+	})
+
+	return f
+}

pkg/obichunk/subchunks.go

@@ -1,10 +1,11 @@
 package obichunk
 
 import (
-	"log"
 	"sort"
 	"sync/atomic"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )
@@ -100,7 +101,7 @@ func ISequenceSubChunk(iterator obiiter.IBioSequenceBatch,
 				classifier.Reset()
 
 				if cap(ordered) < batch.Length() {
-					log.Println("Allocate a new ordered sequences : ", batch.Length())
+					log.Debugln("Allocate a new ordered sequences : ", batch.Length())
 					ordered = make([]sSS, batch.Length())
 				} else {
 					ordered = ordered[:batch.Length()]

pkg/obichunk/unique.go

@@ -3,6 +3,8 @@ package obichunk
 import (
 	"sync"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )
@@ -16,6 +18,10 @@ func IUniqueSequence(iterator obiiter.IBioSequenceBatch,
 
 	iUnique := obiiter.MakeIBioSequenceBatch(opts.BufferSize())
 
+	iterator = iterator.Speed("Splitting data set")
+
+	log.Infoln("Starting data splitting")
+
 	if opts.SortOnDisk() {
 		nworkers = 1
 		iterator, err = ISequenceChunkOnDisk(iterator,
@@ -36,6 +42,8 @@ func IUniqueSequence(iterator obiiter.IBioSequenceBatch,
 		}
 	}
 
+	log.Infoln("End of the data splitting")
+
 	iUnique.Add(nworkers)
 
 	go func() {
@@ -83,7 +91,12 @@ func IUniqueSequence(iterator obiiter.IBioSequenceBatch,
 			batch := input.Get()
 
 			if icat < 0 || len(batch.Slice()) == 1 {
+				if opts.NoSingleton() && len(batch.Slice()) == 1 && batch.Slice()[0].Count() == 1 {
+					batch.Slice()[0].Recycle()
+					batch.Recycle()
+				} else {
 					iUnique.Push(batch.Reorder(nextOrder()))
+				}
 			} else {
 				next.Push(batch.Reorder(o))
 				o++
@@ -111,5 +124,5 @@ func IUniqueSequence(iterator obiiter.IBioSequenceBatch,
 		opts.BufferSize(),
 	)
 
-	return iMerged.Speed(), nil
+	return iMerged.Speed("Variants identified"), nil
 }

pkg/obiformats/dispatcher.go

@@ -2,7 +2,7 @@ package obiformats
 
 import (
 	"fmt"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"sync"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"

pkg/obiformats/ecopcr_read.go

@@ -5,7 +5,7 @@ import (
 	"encoding/csv"
 	"fmt"
 	"io"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"os"
 	"strconv"
 	"strings"

pkg/obiformats/embl_read.go

@@ -5,7 +5,7 @@ import (
 	"bytes"
 	"compress/gzip"
 	"io"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"os"
 	"strconv"
 	"strings"

pkg/obiformats/fastseq_json_header.go

@@ -1,7 +1,7 @@
 package obiformats
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 	"strings"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"

pkg/obiformats/fastseq_read.go

@@ -8,10 +8,11 @@ import "C"
 
 import (
 	"fmt"
-	"log"
 	"os"
 	"unsafe"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/cutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
@@ -100,7 +101,7 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiiter.I
 	fi, err := os.Stat(filename)
 	if err == nil {
 		size = fi.Size()
-		log.Printf("File size of %s is %d bytes\n", filename, size)
+		log.Debugf("File size of %s is %d bytes\n", filename, size)
 	} else {
 		size = -1
 	}
@@ -110,10 +111,10 @@ func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiiter.I
 
 	go func() {
 		newIter.WaitAndClose()
-		log.Println("End of the fastq file reading")
+		log.Debugln("End of the fastq file reading")
 	}()
 
-	log.Println("Start of the fastq file reading")
+	log.Debugln("Start of the fastq file reading")
 
 	go _FastseqReader(pointer, newIter, opt.BatchSize())
 	parser := opt.ParseFastSeqHeader()

pkg/obiformats/fastseq_write_fasta.go

@@ -4,10 +4,11 @@ import (
 	"bytes"
 	"fmt"
 	"io"
-	"log"
 	"os"
 	"strings"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )
@@ -114,6 +115,7 @@ func WriteFastaBatch(iterator obiiter.IBioSequenceBatch,
 	go func() {
 		newIter.WaitAndClose()
 		close(chunkchan)
+		log.Debugln("End of the fasta file writing")
 	}()
 
 	ff := func(iterator obiiter.IBioSequenceBatch) {
@@ -128,7 +130,7 @@ func WriteFastaBatch(iterator obiiter.IBioSequenceBatch,
 		newIter.Done()
 	}
 
-	log.Println("Start of the fasta file writing")
+	log.Debugln("Start of the fasta file writing")
 	go ff(iterator)
 	for i := 0; i < nwriters-1; i++ {
 		go ff(iterator.Split())

pkg/obiformats/fastseq_write_fastq.go

@@ -4,10 +4,11 @@ import (
 	"bytes"
 	"fmt"
 	"io"
-	"log"
 	"os"
 	"time"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )
@@ -114,6 +115,7 @@ func WriteFastqBatch(iterator obiiter.IBioSequenceBatch,
 			time.Sleep(time.Millisecond)
 		}
 		close(chunkchan)
+		log.Debugln("End of the fastq file writing")
 	}()
 
 	ff := func(iterator obiiter.IBioSequenceBatch) {
@@ -129,7 +131,7 @@ func WriteFastqBatch(iterator obiiter.IBioSequenceBatch,
 		newIter.Done()
 	}
 
-	log.Println("Start of the fastq file writing")
+	log.Debugln("Start of the fastq file writing")
 	go ff(iterator)
 	for i := 0; i < nwriters-1; i++ {
 		go ff(iterator.Split())

pkg/obiformats/ncbitaxdump/read.go

@@ -5,7 +5,7 @@ import (
 	"encoding/csv"
 	"fmt"
 	"io"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"os"
 	"path"
 	"strconv"

pkg/obiformats/universal_read.go

@@ -4,10 +4,11 @@ import (
 	"bufio"
 	"compress/gzip"
 	"io"
-	"log"
 	"os"
 	"strings"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 )
 
@@ -57,7 +58,7 @@ func ReadSequencesBatchFromFile(filename string,
 	if err != nil {
 		file.Seek(0, 0)
 	} else {
-		log.Printf("File %s is gz compressed ", filename)
+		log.Debugf("File %s is gz compressed ", filename)
 		reader = greader
 	}
 
@@ -72,7 +73,7 @@ func ReadSequencesBatchFromFile(filename string,
 	}
 
 	filetype := GuessSeqFileType(string(tag))
-	log.Printf("File guessed format : %s (tag: %s)",
+	log.Debug("File guessed format : %s (tag: %s)",
 		filetype, (strings.Split(string(tag), "\n"))[0])
 	reader = breader
 

pkg/obiformats/universal_write.go

@@ -3,7 +3,7 @@ package obiformats
 import (
 	"fmt"
 	"io"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"os"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"

pkg/obiiter/batchiterator.go

@@ -2,11 +2,12 @@ package obiiter
 
 import (
 	"fmt"
-	"log"
 	"sync"
 	"sync/atomic"
 	"time"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 	"github.com/tevino/abool/v2"
 )
@@ -413,7 +414,7 @@ func (iterator IBioSequenceBatch) Rebatch(size int, sizes ...int) IBioSequenceBa
 
 func (iterator IBioSequenceBatch) Recycle() {
 
-	log.Println("Start recycling of Bioseq objects")
+	log.Debugln("Start recycling of Bioseq objects")
 	recycled := 0
 	for iterator.Next() {
 		// iterator.Get()
@@ -424,7 +425,7 @@ func (iterator IBioSequenceBatch) Recycle() {
 		}
 		batch.Recycle()
 	}
-	log.Printf("End of the recycling of %d Bioseq objects", recycled)
+	log.Debugf("End of the recycling of %d Bioseq objects", recycled)
 }
 
 func (iterator IBioSequenceBatch) Count(recycle bool) (int, int, int) {
@@ -432,7 +433,7 @@ func (iterator IBioSequenceBatch) Count(recycle bool) (int, int, int) {
 	reads := 0
 	nucleotides := 0
 
-	log.Println("Start counting of Bioseq objects")
+	log.Debugln("Start counting of Bioseq objects")
 	for iterator.Next() {
 		// iterator.Get()
 		batch := iterator.Get()
@@ -447,7 +448,7 @@ func (iterator IBioSequenceBatch) Count(recycle bool) (int, int, int) {
 		}
 		batch.Recycle()
 	}
-	log.Printf("End of the counting of %d Bioseq objects", variants)
+	log.Debugf("End of the counting of %d Bioseq objects", variants)
 	return variants, reads, nucleotides
 }
 

pkg/obiiter/pairedbatchiterator.go

@@ -1,7 +1,7 @@
 package obiiter
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 	"sync"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"

pkg/obiiter/speed.go

@@ -6,7 +6,7 @@ import (
 	"github.com/schollz/progressbar/v3"
 )
 
-func (iterator IBioSequenceBatch) Speed() IBioSequenceBatch {
+func (iterator IBioSequenceBatch) Speed(message ...string) IBioSequenceBatch {
 	newIter := MakeIBioSequenceBatch()
 
 	newIter.Add(1)
@@ -15,13 +15,25 @@ func (iterator IBioSequenceBatch) Speed() IBioSequenceBatch {
 		newIter.WaitAndClose()
 	}()
 
-	bar := progressbar.NewOptions(
+	pbopt := make([]progressbar.Option, 0, 5)
-		-1,
+	pbopt = append(pbopt,
 		progressbar.OptionSetWriter(os.Stderr),
 		progressbar.OptionSetWidth(15),
 		progressbar.OptionShowCount(),
 		progressbar.OptionShowIts(),
-		progressbar.OptionSetDescription("[Sequence Processing]"))
+	)
+
+	if len(message) > 0 {
+		pbopt = append(pbopt,
+			progressbar.OptionSetDescription(message[0]),
+		)
+	} else {
+		pbopt = append(pbopt,
+			progressbar.OptionSetDescription("[Sequence Processing]"),
+		)
+	}
+
+	bar := progressbar.NewOptions(-1, pbopt...)
 
 	go func() {
 
@@ -38,7 +50,6 @@ func (iterator IBioSequenceBatch) Speed() IBioSequenceBatch {
 	return newIter
 }
 
-
 func SpeedPipe() Pipeable {
 	f := func(iterator IBioSequenceBatch) IBioSequenceBatch {
 		return iterator.Speed()

pkg/obiiter/workers.go

@@ -1,7 +1,7 @@
 package obiiter
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )
@@ -39,7 +39,7 @@ func (iterator IBioSequenceBatch) MakeIWorker(worker SeqWorker, sizes ...int) IB
 
 	go func() {
 		newIter.WaitAndClose()
-		log.Println("End of the batch workers")
+		log.Debugln("End of the batch workers")
 
 	}()
 
@@ -54,7 +54,7 @@ func (iterator IBioSequenceBatch) MakeIWorker(worker SeqWorker, sizes ...int) IB
 		newIter.Done()
 	}
 
-	log.Println("Start of the batch workers")
+	log.Debugln("Start of the batch workers")
 	for i := 0; i < nworkers-1; i++ {
 		go f(iterator.Split())
 	}

pkg/obingslibrary/match.go

@@ -3,7 +3,7 @@ package obingslibrary
 import (
 	"errors"
 	"fmt"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"strings"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"

pkg/obioptions/options.go

@@ -2,10 +2,11 @@ package obioptions
 
 import (
 	"fmt"
-	"log"
 	"os"
 	"runtime"
 
+	log "github.com/sirupsen/logrus"
+
 	"github.com/DavidGamba/go-getoptions"
 )
 
@@ -43,10 +44,21 @@ func GenerateOptionParser(optionset ...func(*getoptions.GetOpt)) ArgumentParser
 			log.Printf("CPU number limited to %d", _MaxAllowedCPU)
 		}
 
+		if options.Called("no-singleton") {
+			log.Printf("No singleton option set")
+		}
+
 		if options.Called("help") {
 			fmt.Fprint(os.Stderr, options.Help())
 			os.Exit(1)
 		}
+
+		log.SetLevel(log.InfoLevel)
+		if options.Called("debug") {
+			log.SetLevel(log.DebugLevel)
+			log.Debugln("Switch to debug level logging")
+		}
+
 		return options, remaining, err
 	}
 }

pkg/obiseq/biosequence.go

@@ -2,9 +2,10 @@ package obiseq
 
 import (
 	"crypto/md5"
-	"log"
 	"sync/atomic"
 
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 )
 
@@ -15,7 +16,7 @@ var _MaxInMemSeq = int32(0)
 var _BioLogRate = int(100000)
 
 func LogBioSeqStatus() {
-	log.Printf("@@@@>>>> Created seq : %d Destroyed : %d  In Memory : %d", _NewSeq, _RecycleSeq, _InMemSeq)
+	log.Debugf("Created seq : %d Destroyed : %d  In Memory : %d", _NewSeq, _RecycleSeq, _InMemSeq)
 }
 
 type Quality []uint8

pkg/obiseq/class.go

@@ -3,7 +3,7 @@ package obiseq
 import (
 	"fmt"
 	"hash/crc32"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"strconv"
 	"sync"
 )

pkg/obiseq/merge.go

@@ -2,7 +2,7 @@ package obiseq
 
 import (
 	"fmt"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"strings"
 )
 

pkg/obiseq/predicate.go

@@ -2,7 +2,7 @@ package obiseq
 
 import (
 	"context"
-	"log"
+	log "github.com/sirupsen/logrus"
 
 	"github.com/PaesslerAG/gval"
 )

pkg/obitax/issuubcladeof.go

@@ -1,7 +1,7 @@
 package obitax
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )

pkg/obitax/taxonomy.go

@@ -2,7 +2,7 @@ package obitax
 
 import (
 	"fmt"
-	"log"
+	log "github.com/sirupsen/logrus"
 )
 
 type TaxName struct {

pkg/obitools/obiconvert/sequence_reader.go

@@ -1,7 +1,7 @@
 package obiconvert
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 	"os"
 	"path/filepath"
 	"strings"

pkg/obitools/obiconvert/sequence_writer.go

@@ -1,7 +1,7 @@
 package obiconvert
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"

pkg/obitools/obidistribute/distribute.go

@@ -1,7 +1,7 @@
 package obidistribute
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"

pkg/obitools/obidistribute/options.go

@@ -2,7 +2,7 @@ package obidistribute
 
 import (
 	"fmt"
-	"log"
+	log "github.com/sirupsen/logrus"
 	"strings"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"

pkg/obitools/obimultiplex/demultiplex.go

@@ -1,7 +1,7 @@
 package obimultiplex
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obingslibrary"

pkg/obitools/obipairing/pairing.go

@@ -1,7 +1,7 @@
 package obipairing
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 	"math"
 	"os"
 	"runtime"

pkg/obitools/obipcr/options.go

@@ -1,7 +1,7 @@
 package obipcr
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"

pkg/obitools/obiuniq/options.go

@@ -10,22 +10,29 @@ var _Keys = make([]string, 0, 10)
 var _OnDisk = false
 var _chunks = 100
 var _NAValue = "NA"
+var _NoSingleton = false
 
 func UniqueOptionSet(options *getoptions.GetOpt) {
 	options.StringSliceVar(&_StatsOn, "merge",
 		1, 1,
 		options.Alias("m"),
+		options.ArgName("KEY"),
 		options.Description("Adds a merged attribute containing the list of sequence record ids merged within this group."))
 
 	options.StringSliceVar(&_Keys, "category-attribute",
 		1, 1,
 		options.Alias("c"),
+		options.ArgName("CATEGORY"),
 		options.Description("Adds one attribute to the list of attributes used to define sequence groups (this option can be used several times)."))
 
 	options.StringVar(&_NAValue, "na-value", _NAValue,
+		options.ArgName("NA_NAME"),
 		options.Description("Value used when the classifier tag is not defined for a sequence."))
 
-	options.BoolVar(&_OnDisk, "on-disk", true,
+	options.BoolVar(&_NoSingleton, "no-singleton", _NoSingleton,
+		options.Description("If set, sequences occurring a single time in the data set are discarded."))
+
+	options.BoolVar(&_OnDisk, "on-disk", _OnDisk,
 		options.Description("Allows for using a disk cache during the dereplication process. "))
 
 	options.IntVar(&_chunks, "chunk-count", _chunks,
@@ -49,7 +56,7 @@ func CLIKeys() []string {
 }
 
 func CLIUniqueInMemory() bool {
-	return _OnDisk
+	return !_OnDisk
 }
 
 func CLINumberOfChunks() int {
@@ -63,3 +70,7 @@ func CLINumberOfChunks() int {
 func CLINAValue() string {
 	return _NAValue
 }
+
+func CLINoSingleton() bool {
+	return _NoSingleton
+}

pkg/obitools/obiuniq/unique.go

@@ -1,7 +1,7 @@
 package obiuniq
 
 import (
-	"log"
+	log "github.com/sirupsen/logrus"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obichunk"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
@@ -24,6 +24,13 @@ func Unique(sequences obiiter.IBioSequenceBatch) obiiter.IBioSequenceBatch {
 		options = append(options, obichunk.OptionSortOnDisk())
 	}
 
+	if CLINoSingleton() {
+		log.Printf("Removing sigletons from the output")
+		options = append(options, obichunk.OptionsNoSingleton())
+	} else {
+		log.Printf("Keep sigletons in the output")
+	}
+
 	options = append(options,
 		obichunk.OptionStatOn(CLIStatsOn()...))