From 8b70b1a5d8c245e981b8c00df81022ef5c422c51 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Wed, 8 Feb 2023 13:56:50 +0100
Subject: [PATCH] Last bug on sequence writing

---
 pkg/obiformats/fastseq_write_fasta.go | 5 +++++
 pkg/obiformats/fastseq_write_fastq.go | 7 +++++++
 2 files changed, 12 insertions(+)

diff --git a/pkg/obiformats/fastseq_write_fasta.go b/pkg/obiformats/fastseq_write_fasta.go
index 404c03a..4db2ef7 100644
--- a/pkg/obiformats/fastseq_write_fasta.go
+++ b/pkg/obiformats/fastseq_write_fasta.go
@@ -6,6 +6,7 @@ import (
 	"io"
 	"os"
 	"strings"
+	"sync"
 	"time"
 
 	log "github.com/sirupsen/logrus"
@@ -78,6 +79,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
 	header_format := opt.FormatFastSeqHeader()
 
 	newIter.Add(nwriters)
+	var waitWriter sync.WaitGroup
 
 	go func() {
 		newIter.WaitAndClose()
@@ -85,6 +87,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
 			time.Sleep(time.Millisecond)
 		}
 		close(chunkchan)
+		waitWriter.Wait()
 		obiiter.UnregisterPipe()
 		log.Debugln("End of the fasta file writing")
 	}()
@@ -112,6 +115,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
 	next_to_send := 0
 	received := make(map[int]FileChunck, 100)
 
+	waitWriter.Add(1)
 	go func() {
 		for chunk := range chunkchan {
 			if chunk.order == next_to_send {
@@ -136,6 +140,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
 				file.Close()
 			}
 		}
+		waitWriter.Done()
 
 	}()
 
diff --git a/pkg/obiformats/fastseq_write_fastq.go b/pkg/obiformats/fastseq_write_fastq.go
index 9f37aff..403fe6a 100644
--- a/pkg/obiformats/fastseq_write_fastq.go
+++ b/pkg/obiformats/fastseq_write_fastq.go
@@ -5,6 +5,7 @@ import (
 	"fmt"
 	"io"
 	"os"
+	"sync"
 	"time"
 
 	log "github.com/sirupsen/logrus"
@@ -69,12 +70,15 @@ func WriteFastq(iterator obiiter.IBioSequence,
 
 	newIter.Add(nwriters)
 
+	var waitWriter sync.WaitGroup
+
 	go func() {
 		newIter.WaitAndClose()
 		for len(chunkchan) > 0 {
 			time.Sleep(time.Millisecond)
 		}
 		close(chunkchan)
+		waitWriter.Wait()
 		obiiter.UnregisterPipe()
 		log.Debugln("End of the fastq file writing")
 	}()
@@ -101,6 +105,7 @@ func WriteFastq(iterator obiiter.IBioSequence,
 	next_to_send := 0
 	received := make(map[int]FileChunck, 100)
 
+	waitWriter.Add(1)
 	go func() {
 		for chunk := range chunkchan {
 			if chunk.order == next_to_send {
@@ -125,6 +130,8 @@ func WriteFastq(iterator obiiter.IBioSequence,
 				file.Close()
 			}
 		}
+
+		waitWriter.Done()
 	}()
 
 	return newIter, nil