From d04161a0fb4bad7143e7271e7f635574eafdda1f Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Tue, 23 Aug 2022 15:08:35 +0200
Subject: [PATCH] small code refactoring

---
 pkg/obiiter/batchiterator.go             | 18 ++++--------------
 pkg/obitools/obidistribute/distribute.go |  6 +++---
 2 files changed, 7 insertions(+), 17 deletions(-)

diff --git a/pkg/obiiter/batchiterator.go b/pkg/obiiter/batchiterator.go
index c1873e7..938a159 100644
--- a/pkg/obiiter/batchiterator.go
+++ b/pkg/obiiter/batchiterator.go
@@ -8,6 +8,7 @@ import (
 
 	log "github.com/sirupsen/logrus"
 
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 	"github.com/tevino/abool/v2"
 )
@@ -37,7 +38,7 @@ type IBioSequenceBatch struct {
 var NilIBioSequenceBatch = IBioSequenceBatch{pointer: nil}
 
 func MakeIBioSequenceBatch(sizes ...int) IBioSequenceBatch {
-	buffsize := int32(1)
+	buffsize := int32(0)
 
 	if len(sizes) > 0 {
 		buffsize = int32(sizes[0])
@@ -215,7 +216,7 @@ func (iterator IBioSequenceBatch) Get() BioSequenceBatch {
 
 func (iterator IBioSequenceBatch) Push(batch BioSequenceBatch) {
 	if batch.IsNil() {
-		log.Panicln("An Nil batch is pushed on the channel")
+		log.Panicln("A Nil batch is pushed on the channel")
 	}
 	if batch.Length() == 0 {
 		log.Panicln("An empty batch is pushed on the channel")
@@ -369,18 +370,7 @@ func (iterator IBioSequenceBatch) Pool(iterators ...IBioSequenceBatch) IBioSeque
 		return iterator
 	}
 
-	counterMutex := sync.Mutex{}
-	counter := 0
-
-	nextCounter := func() int {
-		counterMutex.Lock()
-		defer counterMutex.Unlock()
-
-		counter++
-
-		return counter
-	}
-
+	nextCounter := goutils.AtomicCounter()
 	buffsize := iterator.BufferSize()
 	newIter := MakeIBioSequenceBatch(buffsize)
 
diff --git a/pkg/obitools/obidistribute/distribute.go b/pkg/obitools/obidistribute/distribute.go
index 0dacdf2..1eb1c94 100644
--- a/pkg/obitools/obidistribute/distribute.go
+++ b/pkg/obitools/obidistribute/distribute.go
@@ -13,7 +13,7 @@ func DistributeSequence(sequences obiiter.IBioSequenceBatch) {
 
 	opts := make([]obiformats.WithOption, 0, 10)
 
-	switch obiconvert.OutputFastHeaderFormat() {
+	switch obiconvert.CLIOutputFastHeaderFormat() {
 	case "json":
 		log.Println("On output use JSON headers")
 		opts = append(opts, obiformats.OptionsFastSeqHeaderFormat(obiformats.FormatFastSeqJsonHeader))
@@ -34,11 +34,11 @@ func DistributeSequence(sequences obiiter.IBioSequenceBatch) {
 	opts = append(opts, obiformats.OptionsBufferSize(obioptions.CLIBufferSize()))
 	opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
 
-	opts = append(opts, obiformats.OptionsQualityShift(obiconvert.OutputQualityShift()))
+	opts = append(opts, obiformats.OptionsQualityShift(obiconvert.CLIOutputQualityShift()))
 
 	var formater obiformats.SequenceBatchWriterToFile
 
-	switch obiconvert.OutputFormat() {
+	switch obiconvert.CLIOutputFormat() {
 	case "fastq":
 		formater = obiformats.WriteFastqBatchToFile
 	case "fasta":