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added new extend_path_algorithm
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renamed to extend_haplotypes
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@hfr1tz3 @petrelharp
hfr1tz3 authored and petrelharp committed Sep 18, 2024
1 parent 4170933 commit 659218e
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Showing 11 changed files with 2,027 additions and 922 deletions.
163 changes: 144 additions & 19 deletions c/tests/test_trees.c
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Original file line number Diff line number Diff line change
Expand Up @@ -8414,7 +8414,7 @@ test_split_edges_errors(void)
}

static void
test_extend_edges_simple(void)
test_extend_haplotypes_simple(void)
{
int ret;
tsk_treeseq_t ts, ets;
Expand All @@ -8429,16 +8429,16 @@ test_extend_edges_simple(void)
"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);
ret = tsk_treeseq_extend_haplotypes(&ts, 10, 0, &ets);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_TRUE(tsk_table_collection_equals(ts.tables, ets.tables, 0));
CU_ASSERT_TRUE_FATAL(tsk_table_collection_equals(ts.tables, ets.tables, 0));
tsk_treeseq_free(&ts);

tsk_treeseq_free(&ets);
}

static void
test_extend_edges_errors(void)
test_extend_haplotypes_errors(void)
{
int ret;
tsk_treeseq_t ts, ets;
Expand All @@ -8458,19 +8458,19 @@ test_extend_edges_errors(void)
"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);
ret = tsk_treeseq_extend_haplotypes(&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);
ret = tsk_treeseq_extend_haplotypes(&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);
ret = tsk_treeseq_extend_haplotypes(&ts, 10, 0, &ets);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_DISALLOWED_UNKNOWN_MUTATION_TIME);
tsk_treeseq_free(&ts);

Expand Down Expand Up @@ -8503,17 +8503,21 @@ assert_equal_except_edges_and_mutation_nodes(
}

static void
test_extend_edges(void)
test_extend_haplotypes(void)
{
int ret, max_iter;
int ret = 0;
int max_iter = 10;
tsk_treeseq_t ts, ets;
/* 7 and 8 should be extended to the whole sequence
FILE *tmp = fopen(_tmp_file_name, "w");

/* 7 and 8 should be extended to the whole sequence;
* also 5 to the second tree (where x's are)
6 6 6 6
+-+-+ +-+-+ +-+-+ +-+-+
| | 7 | | 8 | |
| | 7 x x 8 x x
| | ++-+ | | +-++ | |
4 5 4 | | 4 | 5 4 5
4 5 4 | x 4 | 5 4 5
+++ +++ +++ | | | | +++ +++ +++
0 1 2 3 0 1 2 3 0 1 2 3 0 1 2 3
*/
Expand Down Expand Up @@ -8550,26 +8554,144 @@ test_extend_edges(void)
"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";
"1 6 3 -1 3.5\n"
"1 5 1 2 2.5\n"
"1 5 2 3 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);
ret = tsk_treeseq_extend_haplotypes(&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);
ret = tsk_treeseq_extend_haplotypes(&ts, max_iter, 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);
assert_equal_except_edges_and_mutation_nodes(&ts, &ets);
tsk_treeseq_free(&ets);

tsk_set_debug_stream(tmp);
ret = tsk_treeseq_extend_haplotypes(&ts, max_iter, TSK_DEBUG, &ets);
tsk_set_debug_stream(stdout);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_TRUE(ftell(tmp) > 0);
tsk_treeseq_free(&ets);

fclose(tmp);
tsk_treeseq_free(&ts);
}

static void
test_extend_haplotypes_conflicting_times(void)
{
int ret;
int max_iter = 10;
tsk_treeseq_t ts, ets;
/*
3.00┊ 3 ┊ 4 ┊
┊ ┃ ┊ ┃ ┊
2.00┊ ┃ ┊ 2 ┊
┊ ┃ ┊ ┃ ┊
1.00┊ 1 ┊ ┃ ┊
┊ ┃ ┊ ┃ ┊
0.00┊ 0 ┊ 0 ┊
0 2 4
*/

const char *nodes = "1 0.0 -1 -1\n"
"0 1.0 -1 -1\n"
"0 2.0 -1 -1\n"
"0 3.0 -1 -1\n"
"0 3.0 -1 -1\n";
// l, r, p, c
const char *edges = "0.0 2.0 1 0\n"
"2.0 4.0 2 0\n"
"0.0 2.0 3 1\n"
"2.0 4.0 4 2\n";

tsk_treeseq_from_text(&ts, 4, nodes, edges, NULL, NULL, NULL, NULL, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ts.tables->edges.num_rows, 4);

ret = tsk_treeseq_extend_haplotypes(&ts, max_iter, 0, &ets);
CU_ASSERT_EQUAL_FATAL(ret, 0);
CU_ASSERT_TRUE(tsk_table_collection_equals(ts.tables, ets.tables, 0));
tsk_treeseq_free(&ets);

tsk_treeseq_free(&ts);
}

static void
test_extend_haplotypes_new_edge(void)
{
int ret;
int max_iter = 10;
tsk_treeseq_t ts, ets, ref_ts;
/* This is an example where new edges are added
* on both forwards and back passes
4.00┊ ┊ 4 ┊ 4 ┊ 4 ┊
┊ ┊ ┃ ┊ ┃ ┊ ┃ ┊
3.00┊ 2 ┊ ┃ ┊ 2 ┊ 2 ┊
┊ ┃ ┊ ┃ ┊ ┃ ┊ ┃ ┊
2.00┊ ┃ ┊ 3 ┊ ┃ ┊ 3 ┊
┊ ┃ ┊ ┃ ┊ ┃ ┊ ┃ ┊
1.00┊ 1 ┊ ┃ ┊ ┃ ┊ ┃ ┊
┊ ┃ ┊ ┃ ┊ ┃ ┊ ┃ ┊
0.00┊ 0 ┊ 0 ┊ 0 ┊ 0 ┊
0 2 4 6 8
*/

const char *nodes = "1 0.0 -1 -1\n"
"0 1.0 -1 -1\n"
"0 3.0 -1 -1\n"
"0 2.0 -1 -1\n"
"0 4.0 -1 -1\n";
// l, r, p, c
const char *edges = "0.0 2.0 1 0\n"
"2.0 4.0 3 0\n"
"6.0 8.0 3 0\n"
"4.0 5.0 2 0\n"
"5.0 6.0 2 0\n"
"0.0 2.0 2 1\n"
"6.0 7.0 2 3\n"
"7.0 8.0 2 3\n"
"4.0 8.0 4 2\n"
"2.0 4.0 4 3\n";
const char *ext_edges = "0.0 8.0 1 0\n"
"0.0 8.0 3 1\n"
"0.0 8.0 2 3\n"
"2.0 8.0 4 2\n";
const char *sites = "3.0 0\n";
// s, n , ds, t
const char *mutations = "0 4 5 -1 4.5\n"
"0 3 4 0 3.5\n"
"0 3 3 1 2.5\n"
"0 0 2 2 1.5\n"
"0 0 1 3 0.5\n";
const char *ext_mutations = "0 4 5 -1 4.5\n"
"0 2 4 0 3.5\n"
"0 3 3 1 2.5\n"
"0 1 2 2 1.5\n"
"0 0 1 3 0.5\n";

tsk_treeseq_from_text(&ts, 8, nodes, edges, NULL, sites, mutations, NULL, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ts.tables->edges.num_rows, 10);
tsk_treeseq_from_text(
&ref_ts, 8, nodes, ext_edges, NULL, sites, ext_mutations, NULL, NULL, 0);
CU_ASSERT_EQUAL_FATAL(ref_ts.tables->edges.num_rows, 4);

ret = tsk_treeseq_extend_haplotypes(&ts, max_iter, 0, &ets);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_equal_except_edges_and_mutation_nodes(&ts, &ets);
CU_ASSERT_TRUE(tsk_table_collection_equals(ets.tables, ref_ts.tables, 0));
tsk_treeseq_free(&ets);

tsk_treeseq_free(&ts);
tsk_treeseq_free(&ref_ts);
}

static void
Expand Down Expand Up @@ -8793,9 +8915,12 @@ 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_extend_haplotypes_simple", test_extend_haplotypes_simple },
{ "test_extend_haplotypes_errors", test_extend_haplotypes_errors },
{ "test_extend_haplotypes", test_extend_haplotypes },
{ "test_extend_haplotypes_new_edge", test_extend_haplotypes_new_edge },
{ "test_extend_haplotypes_conflicting_times",
test_extend_haplotypes_conflicting_times },
{ "test_init_take_ownership_no_edge_metadata",
test_init_take_ownership_no_edge_metadata },
{ NULL, NULL },
Expand Down
6 changes: 4 additions & 2 deletions c/tests/testlib.c
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
/*
* MIT License
*
* Copyright (c) 2019-2023 Tskit Developers
* Copyright (c) 2019-2024 Tskit Developers
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
Expand Down Expand Up @@ -784,7 +784,9 @@ tsk_treeseq_from_text(tsk_treeseq_t *ts, double sequence_length, const char *nod

ret = tsk_treeseq_init(ts, &tables, TSK_TS_INIT_BUILD_INDEXES);
/* tsk_treeseq_print_state(ts, stdout); */
/* printf("ret = %s\n", tsk_strerror(ret)); */
if (ret != 0) {
printf("\nret = %s\n", tsk_strerror(ret));
}
CU_ASSERT_EQUAL_FATAL(ret, 0);
tsk_table_collection_free(&tables);
}
Expand Down
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