v0.13.1

assembly.go

@@ -58,19 +58,27 @@ func (args assembly) writeHeader(w io.Writer) error {
 
 func (args assembly) writeBody(w io.Writer) error {
 	for _, input := range args.inputs {
-		reader, file, err := getReaderFile(input)
-		if err != nil {
-			return err
-		}
-		defer file.Close()
-		err = assemblyRecords(input, reader, args, w)
+		err := writeBodyLineAssembly(w, input, args)
 		if err != nil {
 			return err
 		}
 	}
 	return nil
 }
 
+func writeBodyLineAssembly(w io.Writer, input string, args assembly) error {
+	reader, file, err := getReaderFile(input)
+	if err != nil {
+		return err
+	}
+	defer file.Close()
+	err = assemblyRecords(input, reader, args, w)
+	if err != nil {
+		return err
+	}
+	return nil
+}
+
 func assemblyRecords(inputPath string, r *Reader, args assembly, w io.Writer) error {
 	contigLengths := make([]int64, 0)
 	var totalLength int64 = 0

cli.go

@@ -13,7 +13,7 @@ var (
 		Use:               "fastats {command}",
 		Short:             "Very simple statistics from fasta files",
 		Long:              ``,
-		Version:           "0.13.0",
+		Version:           "0.13.1",
 		CompletionOptions: cobra.CompletionOptions{DisableDefaultCmd: true},
 		Run: func(cmd *cobra.Command, args []string) {
 			if licences {

content.go

@@ -69,19 +69,27 @@ func (args content) writeHeader(w io.Writer) error {
 
 func (args content) writeBody(w io.Writer) error {
 	for _, input := range args.inputs {
-		reader, file, err := getReaderFile(input)
-		if err != nil {
-			return err
-		}
-		defer file.Close()
-		err = contentRecords(input, reader, args, w)
+		err := writeBodyLineContent(w, input, args)
 		if err != nil {
 			return err
 		}
 	}
 	return nil
 }
 
+func writeBodyLineContent(w io.Writer, input string, args content) error {
+	reader, file, err := getReaderFile(input)
+	if err != nil {
+		return err
+	}
+	defer file.Close()
+	err = contentRecords(input, reader, args, w)
+	if err != nil {
+		return err
+	}
+	return nil
+}
+
 func contentRecords(inputPath string, r *Reader, args content, w io.Writer) error {
 
 	// initiate a count for the total length of the file
@@ -92,7 +100,7 @@ func contentRecords(inputPath string, r *Reader, args content, w io.Writer) erro
 
 	// iterate over every record in the fasta file
 	for {
-		record, err := r.Read()
+		record, err := r.ReadCalcBaseCounts()
 		if err == io.EOF {
 			break
 		}

fasta.go

@@ -33,9 +33,18 @@ func NewZReader(f io.Reader) *Reader {
 	return &Reader{bufio.NewReader(rz)}
 }
 
-// Read reads one fasta record's info from the underlying reader. The final record is returned with error = nil,
-// and the next call to Read() returns an empty Record struct and error = io.EOF.
 func (r *Reader) Read() (Record, error) {
+	return r.read(false)
+}
+
+func (r *Reader) ReadCalcBaseCounts() (Record, error) {
+	return r.read(true)
+}
+
+// read reads one fasta record's info from the underlying reader. The final record is returned with error = nil,
+// and the next call to read() returns an empty Record struct and error = io.EOF.
+// Base content is optionally counted
+func (r *Reader) read(calcBaseCounts bool) (Record, error) {
 
 	var (
 		line, peek []byte
@@ -120,8 +129,10 @@ func (r *Reader) Read() (Record, error) {
 				line = line[:len(line)-drop]
 			}
 
-			for _, b := range line {
-				bases[b]++
+			if calcBaseCounts {
+				for _, b := range line {
+					bases[b]++
+				}
 			}
 			seqLength += int64(len(line))
 		}

fasta_test.go

@@ -34,7 +34,7 @@ AT
 		BaseCounts:  bc,
 	}
 
-	record, err := r.Read()
+	record, err := r.ReadCalcBaseCounts()
 	if err != nil {
 		t.Error(err)
 	}
@@ -53,7 +53,7 @@ AT
 		Len:         20,
 		BaseCounts:  bc,
 	}
-	record, err = r.Read()
+	record, err = r.ReadCalcBaseCounts()
 	if err != nil {
 		t.Error(err)
 	}
@@ -72,7 +72,7 @@ AT
 		Len:         2,
 		BaseCounts:  bc,
 	}
-	record, err = r.Read()
+	record, err = r.ReadCalcBaseCounts()
 	if err != nil {
 		t.Error(err)
 	}
@@ -82,7 +82,7 @@ AT
 	}
 
 	expected = Record{}
-	record, err = r.Read()
+	record, err = r.ReadCalcBaseCounts()
 	if !errors.Is(err, io.EOF) {
 		t.Error(err)
 	}

len.go

@@ -48,19 +48,27 @@ func (args length) writeHeader(w io.Writer) error {
 
 func (args length) writeBody(w io.Writer) error {
 	for _, input := range args.inputs {
-		reader, file, err := getReaderFile(input)
-		if err != nil {
-			return err
-		}
-		defer file.Close()
-		err = lengthRecords(input, reader, args, w)
+		err := writeBodyLineLen(w, input, args)
 		if err != nil {
 			return err
 		}
 	}
 	return nil
 }
 
+func writeBodyLineLen(w io.Writer, input string, args length) error {
+	reader, file, err := getReaderFile(input)
+	if err != nil {
+		return err
+	}
+	defer file.Close()
+	err = lengthRecords(input, reader, args, w)
+	if err != nil {
+		return err
+	}
+	return nil
+}
+
 func lengthRecords(inputPath string, r *Reader, args length, w io.Writer) error {
 
 	// initiate a count for the length of each record

names.go

@@ -22,19 +22,27 @@ func (args names) writeHeader(w io.Writer) error {
 
 func (args names) writeBody(w io.Writer) error {
 	for _, input := range args.inputs {
-		reader, file, err := getReaderFile(input)
-		if err != nil {
-			return err
-		}
-		defer file.Close()
-		err = namesRecords(input, reader, args, w)
+		err := writeBodyLineNames(w, input, args)
 		if err != nil {
 			return err
 		}
 	}
 	return nil
 }
 
+func writeBodyLineNames(w io.Writer, input string, args names) error {
+	reader, file, err := getReaderFile(input)
+	if err != nil {
+		return err
+	}
+	defer file.Close()
+	err = namesRecords(input, reader, args, w)
+	if err != nil {
+		return err
+	}
+	return nil
+}
+
 func namesRecords(inputPath string, r *Reader, args names, w io.Writer) error {
 
 	// iterate over every record in the fasta file

num.go

@@ -16,19 +16,27 @@ func (args num) writeHeader(w io.Writer) error {
 
 func (args num) writeBody(w io.Writer) error {
 	for _, input := range args.inputs {
-		reader, file, err := getReaderFile(input)
-		if err != nil {
-			return err
-		}
-		defer file.Close()
-		err = numRecords(input, reader, args, w)
+		err := writeBodyLineNum(w, input, args)
 		if err != nil {
 			return err
 		}
 	}
 	return nil
 }
 
+func writeBodyLineNum(w io.Writer, input string, args num) error {
+	reader, file, err := getReaderFile(input)
+	if err != nil {
+		return err
+	}
+	defer file.Close()
+	err = numRecords(input, reader, args, w)
+	if err != nil {
+		return err
+	}
+	return nil
+}
+
 func numRecords(inputPath string, r *Reader, args num, w io.Writer) error {
 	// initiate a count for the number of records
 	var c_total int64 = 0