Patch the empty batch bug

Former-commit-id: fcee04b58f2c4a0bf2c27792f991391c0b6ce78e

pkg/obiformats/fastseq_write_fasta.go

@@ -69,6 +69,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
 	options ...WithOption) (obiiter.IBioSequence, error) {
 	opt := MakeOptions(options)
 
+	iterator = iterator.Rebatch(10000)
 	file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
 
 	newIter := obiiter.MakeIBioSequence()

pkg/obiformats/fastseq_write_fastq.go

@@ -56,6 +56,9 @@ type FileChunck struct {
 func WriteFastq(iterator obiiter.IBioSequence,
 	file io.WriteCloser,
 	options ...WithOption) (obiiter.IBioSequence, error) {
+
+	iterator = iterator.Rebatch(10000)
+
 	opt := MakeOptions(options)
 
 	file, _ = goutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())

pkg/obiformats/universal_write.go

@@ -14,8 +14,6 @@ func WriteSequence(iterator obiiter.IBioSequence,
 	file io.WriteCloser,
 	options ...WithOption) (obiiter.IBioSequence, error) {
 
-	iterator = iterator.Rebatch(1000)
-
 	ok := iterator.Next()
 
 	if ok {

pkg/obiiter/batchiterator.go

@@ -235,9 +235,9 @@ func (iterator IBioSequence) Push(batch BioSequenceBatch) {
 	if batch.IsNil() {
 		log.Panicln("A Nil batch is pushed on the channel")
 	}
-	if batch.Len() == 0 {
-		log.Panicln("An empty batch is pushed on the channel")
-	}
+	// if batch.Len() == 0 {
+	// 	log.Panicln("An empty batch is pushed on the channel")
+	// }
 
 	iterator.pointer.channel <- batch
 }

pkg/obitools/obiconvert/sequence_reader.go

@@ -138,7 +138,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 			}
 
 			iterator = obiformats.ReadSequencesBatchFromFiles(
-				filenames,
+				list_of_files,
 				reader,
 				nreader,
 				opts...,
@@ -162,34 +162,11 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
 
 		}
 
-		// list_of_files = list_of_files[1:]
-		// others := make([]obiiter.IBioSequenceBatch, 0, len(list_of_files))
-
-		// for _, fn := range list_of_files {
-		// 	r, err := reader(fn, opts...)
-		// 	if err != nil {
-		// 		return obiiter.NilIBioSequenceBatch, err
-		// 	}
-		// 	others = append(others, r)
-		// }
-
-		// if len(others) > 0 {
-		// 	if CLINoInputOrder() {
-		// 		iterator = iterator.Pool(others...)
-		// 	} else {
-		// 		iterator = iterator.Concat(others...)
-		// 	}
-		// }
-
 	}
 
-	// if SequencesToSkip() > 0 {
-	// 	iterator = iterator.Skip(SequencesToSkip())
-	// }
-
-	// if AnalyzeOnly() > 0 {
-	// 	iterator = iterator.Head(AnalyzeOnly())
-	// }
+	if CLIProgressBar() {
+		iterator = iterator.Speed()
+	}
 
 	return iterator, nil
 }

pkg/obitools/obiconvert/sequence_writer.go

@@ -35,9 +35,6 @@ func BuildPairedFileNames(filename string) (string, string) {
 func CLIWriteBioSequences(iterator obiiter.IBioSequence,
 	terminalAction bool, filenames ...string) (obiiter.IBioSequence, error) {
 
-	if CLIProgressBar() {
-		iterator = iterator.Speed()
-	}
 	var newIter obiiter.IBioSequence
 
 	opts := make([]obiformats.WithOption, 0, 10)