Add support for HIC v9 files, weight column and bump version

4dn-dcic / hic2cool

Lightweight converter between hic and cool contact matrices.

MIT License

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Add support for HIC v9 files, weight column and bump version #69

Open VonAlphaBisZulu opened 5 months ago

VonAlphaBisZulu commented 5 months ago

Addressing Issues #59 and #60. Possibly, also issues #56 and #57.

Tested with hic files in test_data to make sure the update doesn't break anything.

VonAlphaBisZulu commented 5 months ago

In the last two commits, support for the weight-column in conversions was added as well, addressing issue #63. The normalization technique used for the weight column can be specified with the -N flag. Values for normalizations KR, VC, VC_SQRT, SCALE or whatever used, are inverted. This is because Cooler itself uses inverted values in the bin columns if the columns are named KR, VC, VC_SQRT (https://github.com/open2c/cooler/blob/742e5c2adf6b6339ad6fcdb3e0a42449ee4e4675/src/cooler/api.py#L348).

VonAlphaBisZulu commented 1 month ago

Anyone looked into this?