![]() CPU version only searches near the diagonal (in order to run in a reasonable amount of time), so it will not include regions far from the diagonal. This will create additional files in addition to the ones created in prior versions. Starting with version 1.12.03, the given pixels are post-processed at each resolution and the results are merged across resolutions. HiCCUPS will then return enrichments for these specified loops for each resolution. Specified_loop_list is an optional positional argument which should point to a Juicebox formatted loop list. Intermediate files created by HiCCUPS (raw pixels from GPU, clustered pixels for each resolution, and FDR thresholds) will also be saved in this directory. These can be disabled using the suppress flag below. ![]() By default, various values critical to the HICCUPS algorithm are saved as attributes for each loop found. Can be visualized directly in Juicebox as a 2D annotation.
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