izlib

Drop in replacement for zlib.h by isa-l.

Usage

• Install Intel(R) Intelligent Storage Acceleration Library
• Replace "zlib.h" with "izlib.h" and re-compile your file (seqtk for example)

Type	Files	Include	Link flag
zlib	zlib.h	"zlib.h"	-lz
izlib	izlib.h, igzip_lib.h (from isa-l)	"izlib.h"	-lisal

Benchmark

• Data

Reads	Bases	Q20_bases	Q30_bases	GC_bases	File size (toy.fq.gz)
59,581,851	2,979,092,550	2,899,802,990	2,710,969,020	1,188,643,406	2,942,110,279

• Command

time seqtk seq -FE toy.fq.gz > /dev/null

• Results

seqtk version	zlib	izlib	speed up
Runtime	1m18.050s	0m23.648s	3.3×

Examples

Read lines of gzipped or plain file using kstring and izlib

• code

#include <stdio.h>
#include <stdlib.h>
#include "izlib.h"
#include "kstring.h"

// alias to gzgets with input order swapped
char *kzgets(char *buf, int siz, gzFile fp) { return gzgets(fp, buf, siz); }

int main(int argc, char *argv[])
{
        kstring_t ks = {0, 0, 0};
        gzFile fp = gzopen(argv[1], "r");
        if (!fp)
        {
                fprintf(stderr, "Error openning file [%s]\n", argv[1]);
                exit(EXIT_FAILURE);
        }
        while (kgetline(&ks, (kgets_func *)kzgets, fp) == 0)
        {
                puts(ks.s);
                ks.l = 0;
        }
        if (ks.m)
                free(ks.s);
        gzclose(fp);
}

• Compile

cc -o a a.c kstring.c -lisal

• Run

time ./a in.gz | wc -l

Credits