Factorize code between fasta and fastq writers

pkg/obiformats/fastseq_write_fasta.go

@@ -7,8 +7,6 @@ import (
 	"io"
 	"os"
 	"strings"
-	"sync"
-	"time"
 
 	log "github.com/sirupsen/logrus"
 
@@ -135,21 +133,16 @@ func WriteFasta(iterator obiiter.IBioSequence,
 
 	nwriters := opt.ParallelWorkers()
 
-	obiiter.RegisterAPipe()
-	chunkchan := make(chan FileChunk)
+	chunkchan := WriteSeqFileChunk(file, opt.CloseFile())
 
 	header_format := opt.FormatFastSeqHeader()
 
 	newIter.Add(nwriters)
-	var waitWriter sync.WaitGroup
 
 	go func() {
 		newIter.WaitAndClose()
-		for len(chunkchan) > 0 {
-			time.Sleep(time.Millisecond)
-		}
 		close(chunkchan)
-		waitWriter.Wait()
+		log.Warnf("Writing fasta file done")
 	}()
 
 	ff := func(iterator obiiter.IBioSequence) {
@@ -159,10 +152,12 @@ func WriteFasta(iterator obiiter.IBioSequence,
 
 			log.Debugf("Formating fasta chunk %d", batch.Order())
 
-			chunkchan <- FileChunk{
-				FormatFastaBatch(batch, header_format, opt.SkipEmptySequence()),
-				batch.Order(),
+			chunkchan <- SeqFileChunk{
+				Source: batch.Source(),
+				Raw:    bytes.NewBuffer(FormatFastaBatch(batch, header_format, opt.SkipEmptySequence())),
+				Order:  batch.Order(),
 			}
+
 			log.Debugf("Fasta chunk %d formated", batch.Order())
 
 			newIter.Push(batch)
@@ -176,39 +171,6 @@ func WriteFasta(iterator obiiter.IBioSequence,
 		go ff(iterator.Split())
 	}
 
-	next_to_send := 0
-	received := make(map[int]FileChunk, 100)
-
-	waitWriter.Add(1)
-	go func() {
-		for chunk := range chunkchan {
-			if chunk.order == next_to_send {
-				file.Write(chunk.text)
-				log.Debugf("Fasta chunk %d written", chunk.order)
-				next_to_send++
-				chunk, ok := received[next_to_send]
-				for ok {
-					file.Write(chunk.text)
-					log.Debugf("Fasta chunk %d written", chunk.order)
-					delete(received, next_to_send)
-					next_to_send++
-					chunk, ok = received[next_to_send]
-				}
-			} else {
-				log.Debugf("Store Fasta chunk %d", chunk.order)
-				received[chunk.order] = chunk
-			}
-
-		}
-
-		file.Close()
-
-		log.Debugln("End of the fasta file writing")
-		obiiter.UnregisterPipe()
-		waitWriter.Done()
-
-	}()
-
 	return newIter, nil
 }
 

pkg/obiformats/fastseq_write_fastq.go

@@ -105,8 +105,7 @@ func WriteFastq(iterator obiiter.IBioSequence,
 
 	nwriters := opt.ParallelWorkers()
 
-	obiiter.RegisterAPipe()
-	chunkchan := make(chan FileChunk)
+	chunkchan := WriteSeqFileChunk(file, opt.CloseFile())
 
 	header_format := opt.FormatFastSeqHeader()
 
@@ -126,9 +125,10 @@ func WriteFastq(iterator obiiter.IBioSequence,
 	ff := func(iterator obiiter.IBioSequence) {
 		for iterator.Next() {
 			batch := iterator.Get()
-			chunk := FileChunk{
-				FormatFastqBatch(batch, header_format, opt.SkipEmptySequence()),
-				batch.Order(),
+			chunk := SeqFileChunk{
+				Source: batch.Source(),
+				Raw:    bytes.NewBuffer(FormatFastqBatch(batch, header_format, opt.SkipEmptySequence())),
+				Order:  batch.Order(),
 			}
 			chunkchan <- chunk
 			newIter.Push(batch)
@@ -142,44 +142,6 @@ func WriteFastq(iterator obiiter.IBioSequence,
 		go ff(iterator.Split())
 	}
 
-	next_to_send := 0
-	received := make(map[int]FileChunk, 100)
-
-	waitWriter.Add(1)
-	go func() {
-		for chunk := range chunkchan {
-			if chunk.order == next_to_send {
-				if chunk.text[0] != '@' {
-					log.Panicln("WriteFastq: FASTQ format error")
-				}
-				file.Write(chunk.text)
-				next_to_send++
-				chunk, ok := received[next_to_send]
-				for ok {
-					if chunk.text[0] != '@' {
-						log.Panicln("WriteFastq: FASTQ format error")
-					}
-					file.Write(chunk.text)
-					delete(received, next_to_send)
-					next_to_send++
-					chunk, ok = received[next_to_send]
-				}
-			} else {
-				if _, ok := received[chunk.order]; ok {
-					log.Panicln("WriteFastq: Two chunks with the same number")
-				}
-				received[chunk.order] = chunk
-			}
-
-		}
-
-		file.Close()
-
-		log.Debugln("End of the fastq file writing")
-		obiiter.UnregisterPipe()
-		waitWriter.Done()
-	}()
-
 	return newIter, nil
 }
 

pkg/obiformats/seqfile_chunk_read.go

@@ -15,7 +15,7 @@ type SeqFileChunkParser func(string, io.Reader) (obiseq.BioSequenceSlice, error)
 
 type SeqFileChunk struct {
 	Source string
-	Raw    io.Reader
+	Raw    *bytes.Buffer
 	Order  int
 }
 

pkg/obiformats/seqfile_chunk_write.go

@@ -0,0 +1,51 @@
+package obiformats
+
+import (
+	"io"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
+
+	log "github.com/sirupsen/logrus"
+)
+
+func WriteSeqFileChunk(
+	writer io.WriteCloser,
+	toBeClosed bool) ChannelSeqFileChunk {
+
+	obiiter.RegisterAPipe()
+
+	chunk_channel := make(ChannelSeqFileChunk)
+
+	go func() {
+		nextToPrint := 0
+		toBePrinted := make(map[int]SeqFileChunk)
+		for chunk := range chunk_channel {
+			if chunk.Order == nextToPrint {
+				_, _ = writer.Write(chunk.Raw.Bytes())
+				nextToPrint++
+
+				chunk, ok := toBePrinted[nextToPrint]
+				for ok {
+					_, _ = writer.Write(chunk.Raw.Bytes())
+					delete(toBePrinted, nextToPrint)
+					nextToPrint++
+					chunk, ok = toBePrinted[nextToPrint]
+				}
+			} else {
+				toBePrinted[chunk.Order] = chunk
+			}
+		}
+
+		if toBeClosed {
+			err := writer.Close()
+			if err != nil {
+				log.Fatalf("Cannot close the writer : %v", err)
+			}
+		}
+
+		obiiter.UnregisterPipe()
+		log.Warnf("The writer has been closed")
+	}()
+
+	return chunk_channel
+}

pkg/obioptions/version.go

@@ -7,7 +7,7 @@ import (
 // TODO: The version number is extracted from git. This induces that the version
 // corresponds to the last commit, and not the one when the file will be
 // commited
-var _Commit = "dfe2fc3"
+var _Commit = "776b8f7"
 var _Version = ""
 
 // Version returns the version of the obitools package.