Patch a bug on writing to stdout, and add clearer error on openning data files

pkg/obiformats/fastseq_write_fasta.go

@@ -183,7 +183,8 @@ func WriteFasta(iterator obiiter.IBioSequence,
 // The function returns the same bio sequence iterator and an error if any occurred.
 func WriteFastaToStdout(iterator obiiter.IBioSequence,
 	options ...WithOption) (obiiter.IBioSequence, error) {
-	options = append(options, OptionDontCloseFile())
+	// options = append(options, OptionDontCloseFile())
+	options = append(options, OptionCloseFile())
 	return WriteFasta(iterator, os.Stdout, options...)
 }
 

pkg/obiformats/fastseq_write_fastq.go

@@ -97,7 +97,6 @@ func WriteFastq(iterator obiiter.IBioSequence,
 	options ...WithOption) (obiiter.IBioSequence, error) {
 
 	opt := MakeOptions(options)
-	iterator = iterator
 
 	file, _ = obiutils.CompressStream(file, opt.CompressedFile(), opt.CloseFile())
 
@@ -147,7 +146,9 @@ func WriteFastq(iterator obiiter.IBioSequence,
 
 func WriteFastqToStdout(iterator obiiter.IBioSequence,
 	options ...WithOption) (obiiter.IBioSequence, error) {
-	options = append(options, OptionDontCloseFile())
+	//	options = append(options, OptionDontCloseFile())
+	options = append(options, OptionCloseFile())
+
 	return WriteFastq(iterator, os.Stdout, options...)
 }
 

pkg/obiformats/seqfile_chunk_write.go

@@ -21,11 +21,21 @@ func WriteSeqFileChunk(
 		toBePrinted := make(map[int]SeqFileChunk)
 		for chunk := range chunk_channel {
 			if chunk.Order == nextToPrint {
-				_, _ = writer.Write(chunk.Raw.Bytes())
+				log.Debugf("Writing chunk: %d of length %d bytes",
+					chunk.Order,
+					len(chunk.Raw.Bytes()))
+
+				n, err := writer.Write(chunk.Raw.Bytes())
+
+				if err != nil {
+					log.Fatalf("Cannot write chunk %d only %d bytes written on %d sended : %v",
+						chunk.Order, n, len(chunk.Raw.Bytes()), err)
+				}
 				nextToPrint++
 
 				chunk, ok := toBePrinted[nextToPrint]
 				for ok {
+					log.Debug("Writing buffered chunk : ", chunk.Order)
 					_, _ = writer.Write(chunk.Raw.Bytes())
 					delete(toBePrinted, nextToPrint)
 					nextToPrint++
@@ -36,6 +46,7 @@ func WriteSeqFileChunk(
 			}
 		}
 
+		log.Debugf("FIle have to be closed : %v", toBeClosed)
 		if toBeClosed {
 			err := writer.Close()
 			if err != nil {

pkg/obiformats/universal_write.go

@@ -45,7 +45,8 @@ func WriteSequence(iterator obiiter.IBioSequence,
 
 func WriteSequencesToStdout(iterator obiiter.IBioSequence,
 	options ...WithOption) (obiiter.IBioSequence, error) {
-	options = append(options, OptionDontCloseFile())
+	// options = append(options, OptionDontCloseFile())
+	options = append(options, OptionCloseFile())
 	return WriteSequence(iterator, os.Stdout, options...)
 }