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relax requirement for map file and fix function call #118

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Merged
ArniFreyrG merged 1 commit into from
Nov 26, 2025
Merged

relax requirement for map file and fix function call #118

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4 changes: 2 additions & 2 deletions src/threads_arg/__main__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ def main():

@main.command()
@click.option("--pgen", required=True, help="Path to input genotypes in pgen format")
@click.option("--map", required=True, help="Path to genotype map in SHAPEIT format")
@click.option("--map", help="Path to genotype map in SHAPEIT format")
@click.option("--recombination_rate", default=1.3e-8, type=float, help="Genome-wide recombination rate. Ignored if a map is passed")
@click.option("--demography", required=True, help="Path to input genotype")
@click.option("--mode", required=True, type=click.Choice(['array', 'wgs']), default="wgs", help="Inference mode (wgs or array)")
Expand All @@ -53,7 +53,7 @@ def main():
@click.option("--mutation_rate", required=True, type=float, default=1.4e-8, help="Genome-wide mutation rate")
@click.option("--num_threads", type=int, default=1, help="Number of computational threads to request")
@click.option("--region", help="Region of genome in chr:start-end format for which ARG is output. The full genotype is still used for inference")
@click.option("--max_sample_batch_size", help="Max number of LS processes run simultaneously per thread", default=None, type=int)
@click.option("--max_sample_batch_size", help="Max number of LS processes run simultaneously per thread", default=None, type=int)
@click.option("--save_metadata", is_flag=True, default=False, help="If specified, the output will include sample/variant metadata (sample IDs, marker names, allele symbols, etc).")
@click.option("--out")
def infer(**kwargs):
Expand Down
5 changes: 2 additions & 3 deletions src/threads_arg/infer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ def partial_viterbi(pgen, mode, num_samples_hap, physical_positions, genetic_pos
else:
raise RuntimeError

# Batching here saves a small amount of memory
# Batching here saves a small amount of memory
num_samples = len(sample_batch)
sample_indices = list(range(num_samples))
num_subsets = int(np.ceil(num_samples / max_sample_batch_size))
Expand Down Expand Up @@ -198,7 +198,7 @@ def threads_infer(pgen, map, recombination_rate, demography, mutation_rate, fit_
genetic_positions, physical_positions = make_recombination_from_map_and_pgen(map, pgen, chrom)
else:
logger.info(f"Using constant recombination rate of {recombination_rate}")
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bunop marked this conversation as resolved.
genetic_positions, physical_positions = make_constant_recombination_from_pgen(pgen, recombination_rate, chrom)
genetic_positions, physical_positions = make_constant_recombination_from_pgen(pgen, recombination_rate)

# Load/set CHR, POS, ID, REF, ALT, QUAL, FILTER
variant_metadata = read_variant_metadata(pgen) if save_metadata else None
Expand Down Expand Up @@ -361,4 +361,3 @@ def matcher_callback(i, g, mask, matcher):

# Save results
logger.info(f"Done in (s): {time.time() - start_time}")

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