NAME

bl_fastq_name_cmp() - Compare read names of two FASTQ objects

LIBRARY

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

SYNOPSIS

size_t  bl_fastq_name_cmp(bl_fastq_t *read1, bl_fastq_t *read2)

ARGUMENTS

read1, read2    FASTQ reads to compare

DESCRIPTION

Compare the read names of two FASTQ reads. This is useful when processing paired-end data, which must be kept in-sync. I.e. if a sequence if removed from a 5' file, the same sequence should be removed from the 3' file whether or not it meets quality minimums.

RETURN VALUES

0 if read1 and read2 have the same name < 0 if read1 name is lexically less than read2 name > 0 if read1 name is lexically greater than read2 name

EXAMPLES

s1 = bl_fastq_read(&fastq_rec[0], tp->instream1);
s2 = bl_fastq_read(&fastq_rec[1], tp->instream2);
if ( (s1 == BL_READ_OK) && (s2 == BL_READ_OK) )
{


    if ( bl_fastq_name_cmp(&fastq_rec[0], &fastq_rec[1]) != 0 )


    {


        fprintf(stderr, "fastq-trim: Paired files out of sync.n");


        trim_close_files(tp);


        exit(EX_DATAERR);


    }


    ...
}