Friday, November 2, 2012

Fwd: Blasted Bioinformatics!?: BGZF - Blocked, Bigger & Better GZIP!

Nice info on this extremely useful random access format.
Fwd: please follow footer link
Blasted Bioinformatics!?: BGZF - Blocked, Bigger & Better GZIP!:
Blasted Bioinformatics!?
Bioinformatics lessons learned the hard way, bugs, gripes, and maybe topical paper reviews too...


BGZF - Blocked, Bigger & Better GZIP!
BAM files are compressed using a variant of GZIP (GNU ZIP), called BGZF (Blocked GNU Zip Format). Anyone who has read the SAM/BAM Specification will have seen the terms BGZF and virtual offsets, but what you may not realize is how general purpose this is for random access to any large compressed file. The take home message is:
BGZF files are bigger than GZIP files, but they are much faster for random access.

Tucked away in samtools' sister tool set tabix is a little command line tool called bgzip (blocked gzip), which lets you compress any file in BGZF format. It also lets you decompress a BGZF file (nothing special here, they are a GZIP variant so you can use gunzip for this if you like). ...

(Original Post: