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Consistent naming of model mut/rec rate
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In line with other recent changes
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gregorgorjanc authored and petrelharp committed Dec 13, 2024
1 parent aaea903 commit 0f6f263
Showing 1 changed file with 4 additions and 4 deletions.
8 changes: 4 additions & 4 deletions stdpopsim/cli.py
Original file line number Diff line number Diff line change
Expand Up @@ -913,13 +913,13 @@ def write_simulation_summary(
gmap = "None" if contig.genetic_map is None else contig.genetic_map.id
# use the model recombination rate, if provided with the demographic model
if model.recombination_rate is not None:
mean_recomb_rate = model.recombination_rate
recomb_rate = model.recombination_rate
logging.info(
"using recombination rate from demographic model "
f"({model.recombination_rate})"
)
else:
mean_recomb_rate = contig.recombination_map.mean_rate
recomb_rate = contig.recombination_map.mean_rate
logging.info(
"using recombination rate from species contig "
f"({contig.recombination_map.mean_rate})"
Expand All @@ -942,8 +942,8 @@ def write_simulation_summary(
dry_run_text += f"{indent}Contig origin: {contig_origin}\n"
dry_run_text += f"{indent}Contig length: {contig_len}\n"
dry_run_text += f"{indent}Contig ploidy: {contig_ploidy}\n"
dry_run_text += f"{indent}Mean mutation rate: {mut_rate}\n"
dry_run_text += f"{indent}Mean recombination rate: {mean_recomb_rate}\n"
dry_run_text += f"{indent}Mutation rate: {mut_rate}\n"
dry_run_text += f"{indent}Recombination rate: {recomb_rate}\n"
dry_run_text += f"{indent}Genetic map: {gmap}\n"
if contig.bacterial_recombination is True:
dry_run_text += (
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