Possible off-by-one bug in derive_rank_cutoff

[scyrusm]

See also here

The following code from ctxcore leads to the perverse situation where setting auc_threshold to 1 will lead to an assertion error: if auc_threshold were 1, rank_cutoff will be equal to total_genes, but rank_threshold has been set to total_genes - 1. So rank_threshold can at most be total_genes - 1, but then in the final line, rank_cutoff is decremented by `. It seems that there was a double attempt to fix the 0- vs 1-indexing discrepancy between python and R, leading to an off-by-one error...

def derive_rank_cutoff(
  auc_threshold: float, total_genes: int, rank_threshold: Optional[int] = None
  ) -> int:
  """
  Get rank cutoff.
  
  :param auc_threshold: The fraction of the ranked genome to take into account for
      the calculation of the Area Under the recovery Curve.
  :param total_genes: The total number of genes ranked.
  :param rank_threshold: The total number of ranked genes to take into account when
      creating a recovery curve.
  :return Rank cutoff.
  """
  
  if not rank_threshold:
      rank_threshold = total_genes - 1
  
  assert (
      0 < rank_threshold < total_genes
  ), f"Rank threshold must be an integer between 1 and {total_genes:d}."
  assert (
      0.0 < auc_threshold <= 1.0
  ), "AUC threshold must be a fraction between 0.0 and 1.0."
  
  # In the R implementation the cutoff is rounded.
  rank_cutoff = int(round(auc_threshold * total_genes))
  assert 0 < rank_cutoff <= rank_threshold, (
      f"An AUC threshold of {auc_threshold:f} corresponds to {rank_cutoff:d} top "                                                                                                                               
      f"ranked genes/regions in the database. Please increase the rank threshold "                                                                                                                               
      "or decrease the AUC threshold."                                                                                                                                                                           
  )                                                                                                                                                                                                              
  # Make sure we have exactly the same AUC values as the R-SCENIC pipeline.                                                                                                                                      
  # In the latter the rank threshold is not included in AUC calculation.                                                                                                                                         
  rank_cutoff -= 1
  return rank_cutoff