NAME

bl_fastq_find_3p_low_qual() - Find start of low-quality 3' end

LIBRARY

#include <biolibc/fastq.h>
-lbiolibc -lxtend

SYNOPSIS

size_t  bl_fastq_find_3p_low_qual(const bl_fastq_t *read, unsigned min_qual,
unsigned phred_base)

ARGUMENTS

read        FASTQ read to be searched
min_qual    Minimum quality of bases to keep
phred_base  Offset into the ISO character set used by PHRED scores
(usually 33 for modern data)

DESCRIPTION

Locate start of a low-quality 3' end in a FASTQ read. This function uses the same algorithm as fastq and cutadapt as of the time of writing. Namely, it starts at the 3' end of the quality string and sums (base quality - minimum quality) while moving in the 5' direction. This sum will be < 0 as long as the average base quality is < minimum quality. It also keeps track of where the minimum of this sum occurs. When the sum becomes > 0, we have reached a point where the average quality of the 3' end is satisfactory, and it is assumed it will remain that way if we continue in the 5' direction. ( Illumina reads tend to drop in quality near the 3' end. ) The location of the minimum sum is then returned, since the average quality of everything in the 5' direction must be satisfactory.

RETURN VALUES

Index of first low-quality base at the 3' end if found, index of NULL terminator otherwise

EXAMPLES

bl_fastq_t  read;
index = bl_fastq_find_3p_low_qual(&read, 20, 33);
bl_fastq_3p_trim(&read, index);