fq_count_approx_buff.go

// CountFastxRecords counts the number of records in a fastx file.
func CountFastxRecords(fh *os.File, buffSize int, format string) int {
        // Start the timer:
        start := time.Now()
        pattern := []byte("\n+\n") // Pattern to look for.
        // Create new buffered reader:
        reader := bufio.NewReaderSize(fh, buffSize)
        // Byte buffer:
        buffer := make([]byte, buffSize)
        // Variable for counting records:
        var records int

        for {
                // Read next line:
                _, err := reader.Read(buffer)
                // Are we at the end of the file?
                if err == io.EOF {
                        break
                }
                // Anything else went wrong?
                checkError(err)
                // Count the number of fastq separator lines in the buffer:
                records += bytes.Count(buffer, pattern) // FIXME: records will be missed!
        }
        // Print out the time needed for counting:
        fmt.Fprintf(os.Stderr, "%d\n", time.Since(start).Microseconds())
        // Return the number of records:
        return records
}