Comment by laurencerowe

5 years ago

In the genomics world, Tabix indices enables similar use cases. An ordered TSV file is compressed in chunks (bgzip) and a Tabix index created to allow range based access by mapping from the index -> chunk. This allows a browser based genome browser zoomed into a section of the genome to fetch information from a multi gigabyte file.

http://www.htslib.org/doc/tabix.html

2 comments

laurencerowe

Reply
Ultimatt  5 years ago

now if only tabix and most hokey bioinformatics formats would die and just be replaced with a formal schema spec in SQLite...

  • laurencerowe  5 years ago

    Honestly I think Tabix's bgzipped TSV is one of the less hokey bioinformatics formats, at least compared to the various custom binary formats floating around.

    For web browser based genome browsers I suspect this (very cool!) sqlite hack would require many more http requests.