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auto_flush_edges #2183

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Jun 7, 2023
Merged

auto_flush_edges #2183

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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,9 @@
- Enable `additional_nodes` and `coalescing_segments_only` flags for `DTWF` and `FIXED_PEDIDGREE` models ({issue}`2129`, {issue}`2133`, {issue}`2167`, {pr}`2176`,
{user}`GertjanBisschop`)

**Maintenance**:
- Automatically flush edges whenever an edge with a different parent is added to the edge buffer. ({issue}`2182`, {pr}`2183`, {user}`GertjanBisschop`)

## [1.2.0] - 2022-05-18

**New features**
Expand Down
11 changes: 5 additions & 6 deletions algorithms.py
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Original file line number Diff line number Diff line change
Expand Up @@ -780,6 +780,11 @@ def store_edge(self, left, right, parent, child):
"""
Stores the specified edge to the output tree sequence.
"""
if len(self.edge_buffer) > 0:
last_edge = self.edge_buffer[-1]
if last_edge.parent != parent:
self.flush_edges()

self.edge_buffer.append(
tskit.Edge(left=left, right=right, parent=parent, child=child)
)
Expand Down Expand Up @@ -1731,7 +1736,6 @@ def census_event(self, time):
for pop in self.P:
for ancestor in pop.iter_ancestors():
seg = ancestor
self.flush_edges()
u = self.tables.nodes.add_row(
time=time, flags=msprime.NODE_IS_CEN_EVENT, population=pop.id
)
Expand All @@ -1757,7 +1761,6 @@ def store_additional_nodes_edges(self, flag, new_node_id, z):
if new_node_id == -1:
new_node_id = self.store_node(z.population, flags=flag)
else:
self.flush_edges()
self.update_node_flag(new_node_id, flag)
self.store_arg_edges(z, new_node_id)
return new_node_id
Expand Down Expand Up @@ -1798,8 +1801,6 @@ def merge_ancestors(self, H, pop_id, label, new_node_id=-1):
coalescence = True
if new_node_id == -1:
new_node_id = self.store_node(pop_id)
else:
self.flush_edges()
# We must also break if the next left value is less than
# any of the right values in the current overlap set.
if left not in self.S:
Expand Down Expand Up @@ -1944,8 +1945,6 @@ def merge_two_ancestors(self, population_index, label, x, y, u=-1):
if u == -1:
self.store_node(population_index)
u = len(self.tables.nodes) - 1
else:
self.flush_edges()
# Put in breakpoints for the outer edges of the coalesced
# segment
left = x.left
Expand Down
29 changes: 11 additions & 18 deletions lib/msprime.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1814,9 +1814,19 @@ msp_store_edge(msp_t *self, double left, double right, tsk_id_t parent, tsk_id_t
{
int ret = 0;
tsk_edge_t *edge;
tsk_edge_t last_edge;
const double *node_time = self->tables->nodes.time;

tsk_bug_assert(parent < (tsk_id_t) self->tables->nodes.num_rows);
if (self->num_buffered_edges > 0) {
last_edge = self->buffered_edges[self->num_buffered_edges - 1];
if (last_edge.parent != parent) {
ret = msp_flush_edges(self);
if (ret != 0) {
goto out;
}
}
}
if (self->num_buffered_edges == self->max_buffered_edges - 1) {
/* Grow the array */
self->max_buffered_edges *= 2;
Expand Down Expand Up @@ -1923,10 +1933,6 @@ msp_store_additional_nodes_edges(msp_t *self, segment_t *z, tsk_id_t u, uint32_t
}
*new_node_id = ret;
} else {
ret = msp_flush_edges(self);
if (ret != 0) {
goto out;
}
// don't mark sample nodes as PASS_THROUGH
if (!(self->tables->nodes.flags[u] == TSK_NODE_IS_SAMPLE
&& flag == MSP_NODE_IS_PASS_THROUGH)) {
Expand Down Expand Up @@ -2928,11 +2934,6 @@ msp_merge_two_ancestors(msp_t *self, population_id_t population_id, label_id_t l
ret = (int) new_node_id;
goto out;
}
} else {
ret = msp_flush_edges(self);
if (ret != 0) {
goto out;
}
}
}
v = new_node_id;
Expand Down Expand Up @@ -3175,11 +3176,6 @@ msp_merge_ancestors(msp_t *self, avl_tree_t *Q, population_id_t population_id,
ret = (int) new_node_id;
goto out;
}
} else {
ret = msp_flush_edges(self);
if (ret != 0) {
goto out;
}
}
}
/* Insert overlap counts for bounds, if necessary */
Expand Down Expand Up @@ -3804,6 +3800,7 @@ msp_reset(msp_t *self)
self->num_rejected_ca_events = 0;
self->num_trapped_re_events = 0;
self->num_multiple_re_events = 0;
self->num_buffered_edges = 0;
memset(self->num_migration_events, 0, N * N * sizeof(size_t));

if (self->start_time < DBL_MAX) {
Expand Down Expand Up @@ -6557,10 +6554,6 @@ msp_census_event(msp_t *self, demographic_event_t *event)

while (seg != NULL) {
// Add an edge to the edge table.
ret = msp_flush_edges(self);
if (ret != 0) {
goto out;
}
ret = tsk_node_table_add_row(&self->tables->nodes,
MSP_NODE_IS_CEN_EVENT, event->time, i, TSK_NULL, NULL, 0);
if (ret < 0) {
Expand Down