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@avantikalal avantikalal commented Aug 6, 2025

Addresses #156

Earlier in get_gc_matched_intervals, the variable genome was reassigned from the genome name (e.g. hg38) to the genome object produced by genomepy and then passed to filter_blacklist. This led to two issues: 1. filter_blacklist may fail as this is not a blacklist file; and 2. If the user supplied a custom blacklist file, it would be ignored.

Here:

  1. The genome object is called genome_obj instead of genome to avoid reassigning the variable name.
  2. The user no longer needs to supply the blacklist file separately to get_gc_matched_intervals; the function automatically tries to identify a blacklist file based on the supplied genome. The argument is removed from tutorial 3 as a result.
  3. A test for get_gc_matched_intervals is added.

@avantikalal avantikalal merged commit 8212562 into main Aug 11, 2025
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3 participants