home | help 
bl_fastq_f...5p_low_qual(3) Library Functions Manual bl_fastq_f...5p_low_qual(3)

NAME
     bl_fastq_find_5p_low_qual() - Find start of low-quality 5' end

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

SYNOPSIS
     size_t  bl_fastq_find_5p_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 end of a low-quality 5' 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 5' end of the quality string and sums (base quality - minimum
     quality) while moving in the 3' 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 5' end is satisfactory,
     and it is assumed it will remain that way if we continue in the  3'  direc-
     tion.   (	Illumina  reads tend to have low quality near the 5' end. )  The
     location of the minimum sum is then returned, since the average quality  of
     everything in the 3' direction must be satisfactory.

RETURN VALUES
     Index  of first low-quality base at the 5' end if found, index of NULL ter-
     minator otherwise

EXAMPLES
     bl_fastq_t  read;

     index = bl_fastq_find_5p_low_qual(&read, 20, 33);
     bl_fastq_5p_trim(&read, index);

SEE ALSO
     bl_fastq_find_adapter_smart(3),		 bl_fastq_find_adapter_exact(3),
     bl_fastq_trim(3)

						     bl_fastq_f...5p_low_qual(3)
home | help