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