3 ms·
For BAM this could be a good place to start: https://www.htslib.org/benchmarks/CRAM.html https://www.htslib.org/benchmarks/CRAM.html Happy to discuss further
by bede 1y ago
For BAM this could be a good place to start: https://www.htslib.org/benchmarks/CRAM.html https://www.htslib.org/benchmarks/CRAM.html
Happy to discuss further
- terrelln 1y agoAmazing, thank you! I will take a look as soon as I get a chance. Looking at the BAM format, it looks like the tokenization portion will be easy. Which means I can focus on the compression side, which is more interesting.
- fwip 1y agoAnother format that might be worth looking at in the bioinformatics world is hdf5. It's sort of a generic file format, often used for storing multiple related large tables. It has some built-in compression (gzip IIRC) but supports plugins. There may be an opportunity to integrate the self-describing nature of the hdf5 format with the self-describing decompression routines of openZL.
- felixhandte 1y agoWanna hop over to https://github.com/facebook/openzl/issues/76 https://github.com/facebook/openzl/issues/76?