Add long_read option to make_fragment_file#471
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Long-read pipelines (e.g. ONT) mark PCR duplicates upstream with tools such as Picard MarkDuplicates, so reads arrive with the BAM duplicate flag (0x400) set. make_fragment_file discarded those reads during filtering, that made frac_duplicates always 0 and every per-fragment count 1.
Add a
long_readflag (default False) that keeps duplicate-flagged reads so SnapATAC2 deduplicates them itself and reports accurate per-fragment counts and frac_duplicates. Default behavior remain unchanged.