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test for time with keep_roots #823

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merged 1 commit into from Sep 1, 2020
Merged

test for time with keep_roots #823

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3 changes: 2 additions & 1 deletion c/tskit/tables.c
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Expand Up @@ -6458,7 +6458,8 @@ simplifier_insert_input_roots(simplifier_t *self)
if (ret != 0) {
goto out;
}
simplifier_map_mutations(self, input_id, x->left, x->right, x->node);
simplifier_map_mutations(
self, input_id, x->left, x->right, output_id);
}
x = x->next;
}
Expand Down
2 changes: 1 addition & 1 deletion python/tests/simplify.py
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Expand Up @@ -482,7 +482,7 @@ def insert_input_roots(self):
while x is not None:
if x.node != output_id:
self.record_edge(x.left, x.right, output_id, x.node)
self.map_mutations(x.left, x.right, input_id, x.node)
self.map_mutations(x.left, x.right, input_id, output_id)
x = x.next
self.flush_edges()
root_time = self.tables.nodes.time[output_id]
Expand Down
44 changes: 29 additions & 15 deletions python/tests/test_topology.py
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Expand Up @@ -3223,24 +3223,27 @@ def test_single_binary_tree_keep_roots_mutations(self):
keep_input_roots=True,
)

def test_map_mutations_with_and_without_roots(self):
def test_place_mutations_with_and_without_roots(self):
nodes_before = """\
id is_sample time
0 1 0
1 0 1
2 0 2
"""
edges_before = """\
left right parent child
0 2 1 0
0 2 2 1
"""
sites = """\
id position ancestral_state
0 1.0 0
"""
mutations_before = """\
site node derived_state
0 0 2
0 1 1
site node derived_state time
0 0 2 0
0 1 1 1
0 2 3 2
"""
# expected result without keep_input_roots
nodes_after = """\
Expand All @@ -3251,20 +3254,26 @@ def test_map_mutations_with_and_without_roots(self):
left right parent child
"""
mutations_after = """\
site node derived_state
0 0 2
0 0 1
site node derived_state time
0 0 2 0
0 0 1 1
0 0 3 2
"""
# expected result with keep_input_roots
nodes_after_keep = nodes_before
nodes_after_keep = """\
id is_sample time
0 1 0
1 0 2
"""
edges_after_keep = """\
left right parent child
0 2 1 0
"""
mutations_after_keep = """\
site node derived_state
0 0 2
0 0 1
site node derived_state time
0 0 2 0
0 0 1 1
0 1 3 2
"""
self.verify_simplify(
samples=[0],
Expand Down Expand Up @@ -5737,7 +5746,8 @@ def verify_keep_input_roots(self, ts, samples):
self.assertEqual(tree_with_roots.children(root), (mrca,))

# Any mutations that were on the path from the old MRCA
# to the root should be mapped to this node.
# to the root should be mapped to this node, and any mutations
# above the root should still be there.
u = new_to_input_map[mrca]
root_path = []
while u != tskit.NULL:
Expand Down Expand Up @@ -5767,8 +5777,11 @@ def verify_keep_input_roots(self, ts, samples):
input_site = input_sites[position]
for input_mutation in input_site.mutations:
if input_mutation.node in root_path:
# The same mutation should exist and be mapped to the
# mrca
new_node = (
mrca if input_mutation.node != input_root else root
)
# The same mutation should exist and be mapped to
# new_node
new_mutation = new_mutations[input_mutation.metadata]
# We have turned filter sites off, so sites should
# be comparable
Expand All @@ -5777,7 +5790,8 @@ def verify_keep_input_roots(self, ts, samples):
new_mutation.derived_state,
input_mutation.derived_state,
)
self.assertEqual(new_mutation.node, mrca)
self.assertEqual(new_mutation.node, new_node)

return ts_with_roots

def test_many_trees(self):
Expand Down
31 changes: 15 additions & 16 deletions python/tests/tsutil.py
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Expand Up @@ -111,27 +111,26 @@ def insert_branch_mutations(ts, mutations_per_branch=1):
for tree in ts.trees():
site = tables.sites.add_row(position=tree.interval[0], ancestral_state="0")
for root in tree.roots:
state = {root: 0}
mutation = {root: -1}
state = {tskit.NULL: 0}
mutation = {tskit.NULL: -1}
stack = [root]
while len(stack) > 0:
u = stack.pop()
stack.extend(tree.children(u))
v = tree.parent(u)
if v != tskit.NULL:
state[u] = state[v]
parent = mutation[v]
for _ in range(mutations_per_branch):
state[u] = (state[u] + 1) % 2
metadata = f"{len(tables.mutations)}".encode()
mutation[u] = tables.mutations.add_row(
site=site,
node=u,
derived_state=str(state[u]),
parent=parent,
metadata=metadata,
)
parent = mutation[u]
state[u] = state[v]
parent = mutation[v]
for _ in range(mutations_per_branch):
state[u] = (state[u] + 1) % 2
metadata = f"{len(tables.mutations)}".encode()
mutation[u] = tables.mutations.add_row(
site=site,
node=u,
derived_state=str(state[u]),
parent=parent,
metadata=metadata,
)
parent = mutation[u]
add_provenance(tables.provenances, "insert_branch_mutations")
return tables.tree_sequence()

Expand Down