fq_count_naive_count.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 := "+\n" // Pattern to look for.
        // Create new buffered reader:
        reader := bufio.NewReaderSize(fh, buffSize)
        // Variable for counting records:
        var records int

        for {
                // Read next line:
                line, err := reader.ReadString('\n')
                // Are we at the end of the file?
                if err == io.EOF {
                        break
                }
                // Anything else went wrong?
                checkError(err)
                // Is this a fastq separator line?
                if line == pattern {
                        records++
                }
        }
        // Print out the time needed for counting:
        fmt.Fprintf(os.Stderr, "%d\n", time.Since(start).Microseconds())
        // Return the number of records:
        return records
}