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open2c / cooler

A cool place to store your Hi-C
https://open2c.github.io/cooler
BSD 3-Clause "New" or "Revised" License
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cooler cload does not accept .lz4-compressed .pairs files #410

Open bskubi opened 7 months ago

bskubi commented 7 months ago

The pairtools library encourages use of .lz4 compression, but I get an invalid start byte error if I try to use .lz4-compressed .pairs as input to cooler cload pairs. This error goes away if I decompress the .lz4 to plaintext and use that instead. The CLI documentation for cooler cload pairs doesn't state which type of compression it accepts, but does say "Accepts compressed files." I'd recommend either supporting .lz4 or clarifying which types of compression it works with.

nvictus commented 7 months ago

Good catch. We specifically support the compression that pandas.read_csv supports, which does not include lz4.