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bl_fastq_...p_low_qual(3) Library Functions Manual bl_fastq_...p_low_qual(3) 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 writ- ing. 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 become > 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' direc- tion 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); SEE ALSO bl_fastq_find_adapter_smart(3), bl_fastq_find_adapter_exact(3), bl_fastq_trim(3) bl_fastq_...p_low_qual(3)
NAME | LIBRARY | SYNOPSIS | ARGUMENTS | DESCRIPTION | RETURN VALUES | EXAMPLES | SEE ALSO
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