idoneal - sequences.go

     1  // The meta package provides some simple convenience functions for dealing with
     2  // FASTQ files.
     3  package meta // import "vimagination.zapto.org/idoneal/pkg/meta"
     4  
     5  import (
     6  	"fmt"
     7  	"io"
     8  )
     9  
    10  // CountSequences returns the number of Sequences in the passed FASTQ formatted
    11  // Reader.
    12  //
    13  // NB: This function acts naively, simply counting the non-blank lines in the
    14  // Reader, and diving by 4.
    15  func CountSequences(r io.Reader) (int, error) {
    16  	lr := cleaner(r)
    17  	var buf [1024]byte
    18  	lineCount := 1
    19  	for {
    20  		n, err := lr.Read(buf[:])
    21  		for _, b := range buf[:n] {
    22  			if b == '\n' {
    23  				lineCount++
    24  			}
    25  		}
    26  		if err == io.EOF {
    27  			break
    28  		} else if err != nil {
    29  			return 0, fmt.Errorf("error while counting sequences: %w", err)
    30  		}
    31  	}
    32  	return lineCount >> 2, nil
    33  }
    34