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extend edges method #2651

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Nov 7, 2023
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extend edges method #2651

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12 changes: 11 additions & 1 deletion c/CHANGELOG.rst
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Original file line number Diff line number Diff line change
@@ -1,3 +1,13 @@
--------
UPCOMING
--------

**Features**

- Add the `tsk_treeseq_extend_edges` method that can compress a tree sequence
by extending edges into adjacent trees and thus creating unary nodes in those
trees (:user:`petrelharp`, :user:`hfr1tze`, :user:`avabamf`, :pr:`2651`).

--------------------
[1.1.2] - 2023-05-17
--------------------
Expand All @@ -24,7 +34,7 @@
(:user:`jeromekelleher`, :issue:`2662`, :pr:`2663`).

- Guarantee that unfiltered tables are not written to unnecessarily
during simplify (:user:`jeromekelleher` :pr:`2619`).
during simplify (:user:`jeromekelleher`, :pr:`2619`).

- Add `x_table_keep_rows` methods to provide efficient in-place table subsetting
(:user:`jeromekelleher`, :pr:`2700`).
Expand Down
162 changes: 162 additions & 0 deletions c/tests/test_trees.c
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Expand Up @@ -8212,6 +8212,165 @@ test_split_edges_errors(void)
tsk_treeseq_free(&ts);
}

static void
test_extend_edges_simple(void)
{
int ret;
tsk_treeseq_t ts, ets;
const char *nodes = "1 0 -1 -1\n"
"1 0 -1 -1\n"
"0 2.0 -1 -1\n";
const char *edges = "0 10 2 0\n"
"0 10 2 1\n";
const char *sites = "0.0 0\n"
"1.0 0\n";
const char *mutations = "0 0 1 -1 0.5\n"
"1 1 1 -1 0.5\n";

tsk_treeseq_from_text(&ts, 10, nodes, edges, NULL, sites, mutations, NULL, NULL, 0);
ret = tsk_treeseq_extend_edges(&ts, 10, 0, &ets);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_TRUE(tsk_table_collection_equals(ts.tables, ets.tables, 0));
tsk_treeseq_free(&ts);

tsk_treeseq_free(&ets);
}

static void
test_extend_edges_errors(void)
{
int ret;
tsk_treeseq_t ts, ets;
const char *nodes = "1 0 -1 -1\n"
"1 0 -1 -1\n"
"0 2.0 -1 -1\n";
const char *edges = "0 10 2 0\n"
"0 10 2 1\n";
const char *sites = "0.0 0\n"
"1.0 0\n";
const char *mutations = "0 0 1 -1 0.5\n"
"1 1 1 -1 0.5\n";
const char *mutations_no_time = "0 0 1 -1\n"
"1 1 1 -1\n";
// left, right, node source, dest, time
const char *migrations = "0 10 0 0 1 0.5\n"
"0 10 0 1 0 1.5\n";

tsk_treeseq_from_text(&ts, 10, nodes, edges, NULL, sites, mutations, NULL, NULL, 0);
ret = tsk_treeseq_extend_edges(&ts, -2, 0, &ets);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_EXTEND_EDGES_BAD_MAXITER);
tsk_treeseq_free(&ts);

tsk_treeseq_from_text(
&ts, 10, nodes, edges, migrations, sites, mutations, NULL, NULL, 0);
ret = tsk_treeseq_extend_edges(&ts, 10, 0, &ets);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_MIGRATIONS_NOT_SUPPORTED);
tsk_treeseq_free(&ts);

tsk_treeseq_from_text(
&ts, 10, nodes, edges, NULL, sites, mutations_no_time, NULL, NULL, 0);
ret = tsk_treeseq_extend_edges(&ts, 10, 0, &ets);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_DISALLOWED_UNKNOWN_MUTATION_TIME);
tsk_treeseq_free(&ts);

tsk_treeseq_free(&ets);
}

static void
assert_equal_except_edges_and_mutation_nodes(
const tsk_treeseq_t *ts1, const tsk_treeseq_t *ts2)
{
tsk_table_collection_t t1, t2;
int ret;

ret = tsk_table_collection_copy(ts1->tables, &t1, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

ret = tsk_table_collection_copy(ts2->tables, &t2, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

tsk_memset(t1.mutations.node, 0, t1.mutations.num_rows * sizeof(*t1.mutations.node));
tsk_memset(t2.mutations.node, 0, t2.mutations.num_rows * sizeof(*t2.mutations.node));

tsk_edge_table_clear(&t1.edges);
tsk_edge_table_clear(&t2.edges);

CU_ASSERT_TRUE(tsk_table_collection_equals(&t1, &t2, 0));

tsk_table_collection_free(&t1);
tsk_table_collection_free(&t2);
}

static void
test_extend_edges(void)
{
int ret, max_iter;
tsk_treeseq_t ts, ets;
/* 7 and 8 should be extended to the whole sequence

6 6 6 6
+-+-+ +-+-+ +-+-+ +-+-+
| | 7 | | 8 | |
| | ++-+ | | +-++ | |
4 5 4 | | 4 | 5 4 5
+++ +++ +++ | | | | +++ +++ +++
0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3
*/

const char *nodes = "1 0 -1 -1\n"
"1 0 -1 -1\n"
"1 0 -1 -1\n"
"1 0 -1 -1\n"
"0 1.0 -1 -1\n"
"0 1.0 -1 -1\n"
"0 3.0 -1 -1\n"
"0 2.0 -1 -1\n"
"0 2.0 -1 -1\n";
// l, r, p, c
const char *edges = "0 10 4 0\n"
"0 5 4 1\n"
"7 10 4 1\n"
"0 2 5 2\n"
"5 10 5 2\n"
"0 2 5 3\n"
"5 10 5 3\n"
"2 5 7 2\n"
"2 5 7 4\n"
"5 7 8 1\n"
"5 7 8 5\n"
"2 5 6 3\n"
"0 2 6 4\n"
"5 10 6 4\n"
"0 2 6 5\n"
"7 10 6 5\n"
"2 5 6 7\n"
"5 7 6 8\n";
const char *sites = "0.0 0\n"
"9.0 0\n";
const char *mutations = "0 4 1 -1 2.5\n"
"0 4 2 0 1.5\n"
"1 5 1 -1 2.5\n"
"1 5 2 2 1.5\n";

tsk_treeseq_from_text(&ts, 10, nodes, edges, NULL, sites, mutations, NULL, NULL, 0);

for (max_iter = 1; max_iter < 10; max_iter++) {
ret = tsk_treeseq_extend_edges(&ts, max_iter, 0, &ets);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_equal_except_edges_and_mutation_nodes(&ts, &ets);
CU_ASSERT_TRUE(ets.tables->edges.num_rows >= 12);
tsk_treeseq_free(&ets);
}

ret = tsk_treeseq_extend_edges(&ts, 10, 0, &ets);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_EQUAL_FATAL(ets.tables->nodes.num_rows, 9);
CU_ASSERT_EQUAL_FATAL(ets.tables->edges.num_rows, 12);
tsk_treeseq_free(&ets);

tsk_treeseq_free(&ts);
}

static void
test_init_take_ownership_no_edge_metadata(void)
{
Expand Down Expand Up @@ -8431,6 +8590,9 @@ main(int argc, char **argv)
{ "test_split_edges_no_populations", test_split_edges_no_populations },
{ "test_split_edges_populations", test_split_edges_populations },
{ "test_split_edges_errors", test_split_edges_errors },
{ "test_extend_edges_simple", test_extend_edges_simple },
{ "test_extend_edges_errors", test_extend_edges_errors },
{ "test_extend_edges", test_extend_edges },
{ "test_init_take_ownership_no_edge_metadata",
test_init_take_ownership_no_edge_metadata },
{ NULL, NULL },
Expand Down
10 changes: 10 additions & 0 deletions c/tskit/core.c
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Expand Up @@ -330,6 +330,11 @@ tsk_strerror_internal(int err)
"values for any single site. "
"(TSK_ERR_MUTATION_TIME_HAS_BOTH_KNOWN_AND_UNKNOWN)";
break;
case TSK_ERR_DISALLOWED_UNKNOWN_MUTATION_TIME:
ret = "Some mutation times are marked 'unknown' for a method that requires "
"no unknown times. (Use compute_mutation_times to add times?) "
"(TSK_ERR_DISALLOWED_UNKNOWN_MUTATION_TIME)";
break;

/* Migration errors */
case TSK_ERR_UNSORTED_MIGRATIONS:
Expand Down Expand Up @@ -615,6 +620,11 @@ tsk_strerror_internal(int err)
"if an individual has nodes from more than one time. "
"(TSK_ERR_INDIVIDUAL_TIME_MISMATCH)";
break;

case TSK_ERR_EXTEND_EDGES_BAD_MAXITER:
ret = "Maximum number of iterations must be positive. "
"(TSK_ERR_EXTEND_EDGES_BAD_MAXITER)";
break;
}
return ret;
}
Expand Down
15 changes: 15 additions & 0 deletions c/tskit/core.h
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Expand Up @@ -500,6 +500,11 @@ the edge on which it occurs, and wasn't TSK_UNKNOWN_TIME.
A single site had a mixture of known mutation times and TSK_UNKNOWN_TIME
*/
#define TSK_ERR_MUTATION_TIME_HAS_BOTH_KNOWN_AND_UNKNOWN -509
/**
Some mutations have TSK_UNKNOWN_TIME in an algorithm where that's
disallowed (use compute_mutation_times?).
*/
#define TSK_ERR_DISALLOWED_UNKNOWN_MUTATION_TIME -510
/** @} */

/**
Expand Down Expand Up @@ -865,6 +870,16 @@ An individual had nodes from more than one time
*/
#define TSK_ERR_INDIVIDUAL_TIME_MISMATCH -1704
/** @} */

/**
@defgroup EXTEND_EDGES_ERROR_GROUP Extend edges errors.
@{
*/
/**
Maximum iteration number (max_iter) must be positive.
*/
#define TSK_ERR_EXTEND_EDGES_BAD_MAXITER -1800
/** @} */
// clang-format on

/* This bit is 0 for any errors originating from kastore */
Expand Down
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