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cooler zoomify should ensure the base resolution is properly balanced #314

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robomics opened this issue Feb 9, 2023 · 0 comments
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@robomics
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robomics commented Feb 9, 2023

When calling cooler zoomify with --balance and custom balance args (e.g. --balance-args='--cis-only') using an already balanced matrix as base resolution, no checks are performed to ensure that the base resolution was balanced with the same settings specified through --balance-args.

for res in resolutions:
uri = outfile + "::resolutions/" + str(res)
if "weight" in api.Cooler(uri).bins():
continue
logger.info(f"Balancing zoom level with bin size {res}")

This can lead to inconsistent balancing (e.g. the base resolution was balanced using genome-wide interactions, while coarser resolutions are balanced with cis interactions only).

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