HiCExplorer
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hicQuickQC CLI quirks
Might it be that you should
- if args.danglingSequence:
+ if args.restrictionCutFile
over here: https://github.com/deeptools/HiCExplorer/blob/c1e9e92773770dad6ddb002ed7f8522b1dfa56ca/hicexplorer/hicQuickQC.py#L120
But all theses if statements might be dropped anyway since the arguments of optional?
Additionally: The CLI help states "The Alternatively, a fixed binSize can be defined instead", but the binSize seems to be hardcoded.