Start to use leveled log

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()...))