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× |
Isa-l's igzip program sometimes complains about big concatenated gzip file. I'm not sure whether the issue resists in the above API. Use at your own risk.
igzip (version 2.30.0) compiled with newer gcc (gcc version 11.2.1 on my end) works without the aforementioned issue.
