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nanoporetech / pore-c

Pore-C support
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multi-way contacts file #39

Open erbon7 opened 3 years ago

erbon7 commented 3 years ago

Hi, I was wondering if the multi-way contacts derived from the alignment file are stored in a dedicated file and if yes which one ? The "alignments.parquet" file contains only filtered pairwise alignments if I understood correctly ? Thx

eharr commented 3 years ago

@erbon7 sorry for the delayed response. In version 0.3.0 there's *.contacts.parquet file with all pairwise contacts. You can use the read_id column to group these to see all the contacts for a given contcatemer/read. Is this what you meant?

erbon7 commented 3 years ago

Thanks Eoghan for the answer. I just have another question. In the preprint there is a graph analysis procedure to select the best alignments. Is the code to do that part of the pore-c distribution ?

eharr commented 3 years ago

Yes - there the 2 functions linked here carry it out: https://github.com/nanoporetech/pore-c/blob/a865b7ea64d7a972fe878e8f9ea4aa7553def363/pore_c/analyses/alignments.py#L181-L230