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First pass on stop_at_local_mrca #2392

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First pass on stop_at_local_mrca #2392

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15 changes: 10 additions & 5 deletions algorithms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -885,6 +885,7 @@ def __init__(
gene_conversion_length=1,
discrete_genome=True,
hull_offset=None,
stop_at_local_mrca=True,
):
# Must be a square matrix.
N = len(migration_matrix)
Expand All @@ -906,6 +907,7 @@ def __init__(
self.migration_matrix = migration_matrix
self.num_labels = num_labels
self.num_populations = N
self.stop_at_local_mrca = stop_at_local_mrca
self.max_segments = max_segments
self.coalescing_segments_only = coalescing_segments_only
self.additional_nodes = msprime.NodeType(additional_nodes)
Expand Down Expand Up @@ -1253,7 +1255,7 @@ def simulate(self, end_time):
if self.model == "hudson":
self.hudson_simulate(end_time)
elif self.model == "dtwf":
self.dtwf_simulate()
self.dtwf_simulate(end_time)
elif self.model == "fixed_pedigree":
self.pedigree_simulate()
elif self.model == "single_sweep":
Expand Down Expand Up @@ -1524,11 +1526,11 @@ def pedigree_simulate(self):
self.pedigree = Pedigree(self.tables)
self.dtwf_climb_pedigree()

def dtwf_simulate(self):
def dtwf_simulate(self, end_time):
"""
Simulates the algorithm until all loci have coalesced.
"""
while self.ancestors_remain():
while self.ancestors_remain() and self.t < end_time:
self.t += 1
self.verify()
self.dtwf_generation()
Expand Down Expand Up @@ -2394,6 +2396,7 @@ def merge_two_ancestors(self, population_index, label, x, y, u=-1):
new_lineage = self.alloc_lineage(None, population_index, label=label)
coalescence = False
defrag_required = False
min_overlap = 0

while x is not None or y is not None:
alpha = None
Expand Down Expand Up @@ -2435,12 +2438,12 @@ def merge_two_ancestors(self, population_index, label, x, y, u=-1):
j = self.S.floor_key(r_max)
self.S[r_max] = self.S[j]
# Update the number of extant segments.
if self.S[left] == 2:
if self.S[left] == min_overlap:
self.S[left] = 0
right = self.S.succ_key(left)
else:
right = left
while right < r_max and self.S[right] != 2:
while right < r_max and self.S[right] != min_overlap:
self.S[right] -= 1
right = self.S.succ_key(right)
alpha = self.alloc_segment(
Expand Down Expand Up @@ -2860,6 +2863,7 @@ def run_simulate(args):
gene_conversion_length=mean_tract_length,
discrete_genome=args.discrete,
hull_offset=args.offset,
stop_at_local_mrca=args.stop_at_local_mrca,
)
ts = s.simulate(args.end_time)
ts.dump(args.output_file)
Expand Down Expand Up @@ -2946,6 +2950,7 @@ def add_simulator_arguments(parser):
help="The delta_t value for selective sweeps",
)
parser.add_argument("--model", default="hudson")
parser.add_argument("--stop-at-local-mrca", default=True, type=bool)
parser.add_argument("--offset", type=float, default=0.0)
parser.add_argument(
"--from-ts",
Expand Down
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