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4dn-dcic / hic2cool

Lightweight converter between hic and cool contact matrices.
MIT License
67 stars 7 forks source link

faster conversion? #42

Closed fanc-WU closed 4 years ago

fanc-WU commented 4 years ago

I'm trying to convert several relatively big .hic files into mcool format. They are around 20G. It took me 18 hours to convert 4.6G. I was wondering if there is a faster way? I didn't see any options to assign multiple threads or increase memory.

Thank you so much and best regards, Fan

SooLee commented 4 years ago

I don't think a faster option is available currently, but it looks like multiprocessing may be possible. I will see if I can implement something over the long weekend.

SooLee commented 4 years ago

hic2cool 0.8.0 has a multiprocessing option now. It is not very efficient though. Would be slightly helpful for large high-resolution matrices.

fanc-WU commented 4 years ago

hic2cool 0.8.0 has a multiprocessing option now. It is not very efficient though. Would be slightly helpful for large high-resolution matrices.

Thank you so much for implementing this! I really appreciate it