add the --skip-empty option

Former-commit-id: ec9cb0ecaf90a61bf9289cf4c089b5cc2fcb65a5

pkg/obiformats/fastseq_write_fasta.go

@@ -55,11 +55,19 @@ func FormatFasta(seq *obiseq.BioSequence, formater FormatHeader) string {
 		folded)
 }
 
-func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader) []byte {
+func FormatFastaBatch(batch obiiter.BioSequenceBatch, formater FormatHeader, skipEmpty bool) []byte {
 	var bs bytes.Buffer
 	for _, seq := range batch.Slice() {
-		bs.WriteString(FormatFasta(seq, formater))
-		bs.WriteString("\n")
+		if seq.Len() > 0 {
+			bs.WriteString(FormatFasta(seq, formater))
+			bs.WriteString("\n")	
+		} else {
+			if skipEmpty {
+				log.Warnf("Sequence %s is empty and skiped in output",seq.Id())
+			} else {
+				log.Fatalf("Sequence %s is empty",seq.Id())
+			}
+		}
 	}
 	return bs.Bytes()
 }
@@ -99,7 +107,7 @@ func WriteFasta(iterator obiiter.IBioSequence,
 			batch := iterator.Get()
 
 			chunkchan <- FileChunck{
-				FormatFastaBatch(batch, header_format),
+				FormatFastaBatch(batch, header_format, opt.SkipEmptySequence()),
 				batch.Order(),
 			}
 			newIter.Push(batch)

pkg/obiformats/fastseq_write_fastq.go

@@ -39,11 +39,20 @@ func FormatFastq(seq *obiseq.BioSequence, quality_shift int, formater FormatHead
 }
 
 func FormatFastqBatch(batch obiiter.BioSequenceBatch, quality_shift int,
-	formater FormatHeader) []byte {
+	formater FormatHeader, skipEmpty bool) []byte {
 	var bs bytes.Buffer
 	for _, seq := range batch.Slice() {
-		bs.WriteString(FormatFastq(seq, quality_shift, formater))
-		bs.WriteString("\n")
+		if seq.Len() > 0 {
+			bs.WriteString(FormatFastq(seq, quality_shift, formater))
+			bs.WriteString("\n")
+		} else {
+			if skipEmpty {
+				log.Warnf("Sequence %s is empty and skiped in output", seq.Id())
+			} else {
+				log.Fatalf("Sequence %s is empty", seq.Id())
+			}
+		}
+
 	}
 	return bs.Bytes()
 }
@@ -90,7 +99,7 @@ func WriteFastq(iterator obiiter.IBioSequence,
 		for iterator.Next() {
 			batch := iterator.Get()
 			chunk := FileChunck{
-				FormatFastqBatch(batch, quality, header_format),
+				FormatFastqBatch(batch, quality, header_format, opt.SkipEmptySequence()),
 				batch.Order(),
 			}
 			chunkchan <- chunk

pkg/obiformats/options.go

@@ -16,6 +16,7 @@ type __options__ struct {
 	closefile             bool
 	appendfile            bool
 	compressed            bool
+	skip_empty            bool
 	csv_id                bool
 	csv_sequence          bool
 	csv_quality           bool
@@ -48,6 +49,7 @@ func MakeOptions(setters []WithOption) Options {
 		closefile:             false,
 		appendfile:            false,
 		compressed:            false,
+		skip_empty:            false,
 		csv_id:                true,
 		csv_definition:        false,
 		csv_count:             false,
@@ -110,6 +112,10 @@ func (opt Options) CompressedFile() bool {
 	return opt.pointer.compressed
 }
 
+func (opt Options) SkipEmptySequence() bool {
+	return opt.pointer.skip_empty
+}
+
 func (opt Options) CSVId() bool {
 	return opt.pointer.csv_id
 }
@@ -194,6 +200,14 @@ func OptionsCompressed(compressed bool) WithOption {
 	return f
 }
 
+func OptionsSkipEmptySequence(skip bool) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.skip_empty = skip
+	})
+
+	return f
+}
+
 func OptionsNewFile() WithOption {
 	f := WithOption(func(opt Options) {
 		opt.pointer.appendfile = false

pkg/obitools/obiclean/obiclean.go

@@ -285,7 +285,7 @@ func Weight(sequence *obiseq.BioSequence) map[string]int {
 	return weight
 }
 
-func IOBIClean(itertator obiiter.IBioSequence) obiiter.IBioSequence {
+func CLIOBIClean(itertator obiiter.IBioSequence) obiiter.IBioSequence {
 
 	db := itertator.Load()
 

pkg/obitools/obiconvert/options.go

@@ -26,6 +26,7 @@ var __output_solexa_quality__ = false
 
 var __no_progress_bar__ = false
 var __compressed__ = false
+var __skip_empty__ = false
 
 var __output_file_name__ = "-"
 var __paired_file_name__ = ""
@@ -70,6 +71,9 @@ func OutputModeOptionSet(options *getoptions.GetOpt) {
 		options.Alias("Z"),
 		options.Description("Output is compressed"))
 
+		options.BoolVar(&__skip_empty__, "skip-empty", __skip_empty__,
+		options.Description("Sequences of length equal to zero are suppressed from the output"))
+
 	options.StringVar(&__output_file_name__, "out", __output_file_name__,
 		options.Alias("o"),
 		options.ArgName("FILENAME"),
@@ -141,6 +145,10 @@ func CLICompressed() bool {
 	return __compressed__
 }
 
+func CLISkipEmpty() bool {
+	return __skip_empty__ 
+}
+
 func CLIInputFastHeaderFormat() string {
 	switch {
 	case __input_fastjson_format__:

pkg/obitools/obiconvert/sequence_writer.go

@@ -80,6 +80,8 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
 			var reverse string
 			fn, reverse = BuildPairedFileNames(fn)
 			opts = append(opts, obiformats.WritePairedReadsTo(reverse))
+		} else {
+			opts = append(opts, obiformats.OptionsSkipEmptySequence(CLISkipEmpty()))
 		}
 
 		switch CLIOutputFormat() {
@@ -91,6 +93,7 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
 			newIter, err = obiformats.WriteSequencesToFile(iterator, fn, opts...)
 		}
 	} else {
+		opts = append(opts, obiformats.OptionsSkipEmptySequence(CLISkipEmpty()))
 		switch CLIOutputFormat() {
 		case "fastq":
 			newIter, err = obiformats.WriteFastqToStdout(iterator, opts...)
@@ -99,6 +102,7 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
 		default:
 			newIter, err = obiformats.WriteSequencesToStdout(iterator, opts...)
 		}
+
 	}
 
 	if err != nil {