Skip to content

Divmat sample_sets #2823

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Jan 16, 2024
Merged

Divmat sample_sets #2823

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
163b86f
Support sample sets in divmat
jeromekelleher Aug 16, 2023
71db20d
Add check for non-single sample sets and disable tests
jeromekelleher Jan 16, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
136 changes: 97 additions & 39 deletions c/tests/test_stats.c
View file
Open in desktop
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 @@ -287,7 +287,8 @@ verify_divergence_matrix(tsk_treeseq_t *ts, tsk_flags_t options)
ts, n, sample_set_sizes, samples, n * n, index_tuples, 0, NULL, options, D1);
CU_ASSERT_EQUAL_FATAL(ret, 0);

ret = tsk_treeseq_divergence_matrix(ts, 0, NULL, 0, NULL, options, D2);
ret = tsk_treeseq_divergence_matrix(
ts, n, sample_set_sizes, samples, 0, NULL, options, D2);
CU_ASSERT_EQUAL_FATAL(ret, 0);

for (j = 0; j < n; j++) {
Expand Down Expand Up @@ -1057,19 +1058,42 @@ test_single_tree_divergence_matrix(void)
int ret;
double result[16];
double D_branch[16] = { 0, 2, 6, 6, 2, 0, 6, 6, 6, 6, 0, 4, 6, 6, 4, 0 };
double D_site[16] = { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 };
double D_site[16] = { 0, 1, 1, 0, 1, 0, 2, 1, 1, 2, 0, 1, 0, 1, 1, 0 };

tsk_treeseq_from_text(&ts, 1, single_tree_ex_nodes, single_tree_ex_edges, NULL, NULL,
NULL, NULL, NULL, 0);
tsk_size_t sample_set_sizes[] = { 2, 2 };

ret = tsk_treeseq_divergence_matrix(&ts, 0, NULL, 0, NULL, TSK_STAT_BRANCH, result);
tsk_treeseq_from_text(&ts, 1, single_tree_ex_nodes, single_tree_ex_edges, NULL,
single_tree_ex_sites, single_tree_ex_mutations, NULL, NULL, 0);

ret = tsk_treeseq_divergence_matrix(
&ts, 0, NULL, NULL, 0, NULL, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(16, result, D_branch);

ret = tsk_treeseq_divergence_matrix(&ts, 0, NULL, 0, NULL, TSK_STAT_SITE, result);
ret = tsk_treeseq_divergence_matrix(
&ts, 0, NULL, NULL, 0, NULL, TSK_STAT_SITE, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(16, result, D_site);

ret = tsk_treeseq_divergence_matrix(
&ts, 2, sample_set_sizes, NULL, 0, NULL, TSK_STAT_SITE, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);

ret = tsk_treeseq_divergence_matrix(
&ts, 2, sample_set_sizes, NULL, 0, NULL, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);

sample_set_sizes[0] = 3;
sample_set_sizes[1] = 1;
ret = tsk_treeseq_divergence_matrix(
&ts, 2, sample_set_sizes, NULL, 0, NULL, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_treeseq_divergence_matrix(
&ts, 2, sample_set_sizes, NULL, 0, NULL, TSK_STAT_SITE, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);

/* assert_arrays_almost_equal(4, result, D_site); */

verify_divergence_matrix(&ts, TSK_STAT_BRANCH);
verify_divergence_matrix(&ts, TSK_STAT_BRANCH | TSK_STAT_SPAN_NORMALISE);
verify_divergence_matrix(&ts, TSK_STAT_SITE);
Expand All @@ -1083,7 +1107,7 @@ test_single_tree_divergence_matrix_internal_samples(void)
{
tsk_treeseq_t ts;
int ret;
double result[16];
double *result = malloc(16 * sizeof(double));
double D[16] = { 0, 2, 4, 3, 2, 0, 4, 3, 4, 4, 0, 1, 3, 3, 1, 0 };

const char *nodes = "1 0 -1 -1\n" /* 2.00┊ 6 ┊ */
Expand All @@ -1109,14 +1133,35 @@ test_single_tree_divergence_matrix_internal_samples(void)
"3 3 T -1\n"
"4 4 T -1\n"
"5 5 T -1\n";
tsk_id_t samples[] = { 0, 1, 2, 5 };
tsk_size_t sizes[] = { 1, 1, 1, 1 };

tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, sites, mutations, NULL, NULL, 0);

ret = tsk_treeseq_divergence_matrix(&ts, 0, NULL, 0, NULL, TSK_STAT_BRANCH, result);
ret = tsk_treeseq_divergence_matrix(
&ts, 0, NULL, NULL, 0, NULL, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(16, result, D);
ret = tsk_treeseq_divergence_matrix(
&ts, 0, NULL, NULL, 0, NULL, TSK_STAT_SITE, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(16, result, D);

ret = tsk_treeseq_divergence_matrix(&ts, 0, NULL, 0, NULL, TSK_STAT_SITE, result);
ret = tsk_treeseq_divergence_matrix(
&ts, 4, sizes, samples, 0, NULL, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(16, result, D);
ret = tsk_treeseq_divergence_matrix(
&ts, 4, sizes, samples, 0, NULL, TSK_STAT_SITE, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(16, result, D);

ret = tsk_treeseq_divergence_matrix(
&ts, 4, NULL, samples, 0, NULL, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(16, result, D);
ret = tsk_treeseq_divergence_matrix(
&ts, 4, NULL, samples, 0, NULL, TSK_STAT_SITE, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(16, result, D);

Expand All @@ -1126,6 +1171,7 @@ test_single_tree_divergence_matrix_internal_samples(void)
verify_divergence_matrix(&ts, TSK_STAT_SITE | TSK_STAT_SPAN_NORMALISE);

tsk_treeseq_free(&ts);
free(result);
}

static void
Expand Down Expand Up @@ -1164,7 +1210,8 @@ test_single_tree_divergence_matrix_multi_root(void)

tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, sites, mutations, NULL, NULL, 0);

ret = tsk_treeseq_divergence_matrix(&ts, 0, NULL, 0, NULL, TSK_STAT_BRANCH, result);
ret = tsk_treeseq_divergence_matrix(
&ts, 0, NULL, NULL, 0, NULL, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(16, result, D_branch);

Expand Down Expand Up @@ -2424,73 +2471,84 @@ test_simplest_divergence_matrix(void)
"1 0 0\n"
"0 1 0\n";
const char *edges = "0 1 2 0,1\n";
const char *sites = "0.1 A\n"
"0.6 A\n";
const char *mutations = "0 0 B -1\n"
"1 0 B -1\n";
tsk_treeseq_t ts;
tsk_id_t sample_ids[] = { 0, 1 };
double D_branch[4] = { 0, 2, 2, 0 };
double D_site[4] = { 0, 0, 0, 0 };
double D_site[4] = { 0, 2, 2, 0 };
double result[4];
int ret;

tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, NULL, NULL, NULL, NULL, 0);
tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, sites, mutations, NULL, NULL, 0);

ret = tsk_treeseq_divergence_matrix(
&ts, 2, sample_ids, 0, NULL, TSK_STAT_BRANCH, result);
&ts, 2, NULL, sample_ids, 0, NULL, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(4, D_branch, result);

ret = tsk_treeseq_divergence_matrix(
&ts, 2, sample_ids, 0, NULL, TSK_STAT_BRANCH | TSK_STAT_SPAN_NORMALISE, result);
ret = tsk_treeseq_divergence_matrix(&ts, 2, NULL, sample_ids, 0, NULL,
TSK_STAT_BRANCH | TSK_STAT_SPAN_NORMALISE, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(4, D_branch, result);

ret = tsk_treeseq_divergence_matrix(&ts, 2, sample_ids, 0, NULL, 0, result);
ret = tsk_treeseq_divergence_matrix(&ts, 2, NULL, sample_ids, 0, NULL, 0, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(4, D_site, result);

ret = tsk_treeseq_divergence_matrix(
&ts, 2, sample_ids, 0, NULL, TSK_STAT_SPAN_NORMALISE, result);
&ts, 2, NULL, sample_ids, 0, NULL, TSK_STAT_SPAN_NORMALISE, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(4, D_site, result);

ret = tsk_treeseq_divergence_matrix(
&ts, 2, sample_ids, 0, NULL, TSK_STAT_SITE, result);
&ts, 2, NULL, sample_ids, 0, NULL, TSK_STAT_SITE, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(4, D_site, result);

ret = tsk_treeseq_divergence_matrix(&ts, 0, NULL, 0, NULL, TSK_STAT_BRANCH, result);
ret = tsk_treeseq_divergence_matrix(
&ts, 0, NULL, NULL, 0, NULL, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(4, D_branch, result);

ret = tsk_treeseq_divergence_matrix(&ts, 0, NULL, 0, NULL, TSK_STAT_SITE, result);
ret = tsk_treeseq_divergence_matrix(
&ts, 0, NULL, NULL, 0, NULL, TSK_STAT_SITE, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(4, D_site, result);

ret = tsk_treeseq_divergence_matrix(&ts, 0, NULL, 0, NULL, TSK_STAT_NODE, result);
ret = tsk_treeseq_divergence_matrix(
&ts, 0, NULL, NULL, 0, NULL, TSK_STAT_NODE, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_UNSUPPORTED_STAT_MODE);

ret = tsk_treeseq_divergence_matrix(
&ts, 0, NULL, 0, NULL, TSK_STAT_POLARISED, result);
&ts, 0, NULL, NULL, 0, NULL, TSK_STAT_POLARISED, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_STAT_POLARISED_UNSUPPORTED);

ret = tsk_treeseq_divergence_matrix(
&ts, 0, NULL, 0, NULL, TSK_STAT_SITE | TSK_STAT_BRANCH, result);
&ts, 0, NULL, NULL, 0, NULL, TSK_STAT_SITE | TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_MULTIPLE_STAT_MODES);

sample_ids[0] = -1;
ret = tsk_treeseq_divergence_matrix(&ts, 2, sample_ids, 0, NULL, 0, result);
ret = tsk_treeseq_divergence_matrix(&ts, 2, NULL, sample_ids, 0, NULL, 0, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_NODE_OUT_OF_BOUNDS);

sample_ids[0] = 3;
ret = tsk_treeseq_divergence_matrix(&ts, 2, sample_ids, 0, NULL, 0, result);
ret = tsk_treeseq_divergence_matrix(&ts, 2, NULL, sample_ids, 0, NULL, 0, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_NODE_OUT_OF_BOUNDS);

sample_ids[0] = 1;
ret = tsk_treeseq_divergence_matrix(&ts, 2, sample_ids, 0, NULL, 0, result);
ret = tsk_treeseq_divergence_matrix(&ts, 2, NULL, sample_ids, 0, NULL, 0, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_DUPLICATE_SAMPLE);
ret = tsk_treeseq_divergence_matrix(
&ts, 2, sample_ids, 0, NULL, TSK_STAT_BRANCH, result);
&ts, 2, NULL, sample_ids, 0, NULL, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_DUPLICATE_SAMPLE);

sample_ids[0] = 2;
ret = tsk_treeseq_divergence_matrix(&ts, 2, NULL, sample_ids, 0, NULL, 0, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_SAMPLES);

tsk_treeseq_free(&ts);
}

Expand All @@ -2515,39 +2573,39 @@ test_simplest_divergence_matrix_windows(void)

tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, sites, mutations, NULL, NULL, 0);

ret = tsk_treeseq_divergence_matrix(&ts, 2, sample_ids, 2, windows, 0, result);
ret = tsk_treeseq_divergence_matrix(&ts, 2, NULL, sample_ids, 2, windows, 0, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(8, D_site, result);
ret = tsk_treeseq_divergence_matrix(
&ts, 2, sample_ids, 2, windows, TSK_STAT_BRANCH, result);
&ts, 2, NULL, sample_ids, 2, windows, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(8, D_branch, result);

/* Windows for the second half */
ret = tsk_treeseq_divergence_matrix(
&ts, 2, sample_ids, 1, windows + 1, TSK_STAT_SITE, result);
&ts, 2, NULL, sample_ids, 1, windows + 1, TSK_STAT_SITE, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(4, D_site, result);
ret = tsk_treeseq_divergence_matrix(
&ts, 2, sample_ids, 1, windows + 1, TSK_STAT_BRANCH, result);
&ts, 2, NULL, sample_ids, 1, windows + 1, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(4, D_branch, result);

ret = tsk_treeseq_divergence_matrix(&ts, 2, sample_ids, 0, windows, 0, result);
ret = tsk_treeseq_divergence_matrix(&ts, 2, NULL, sample_ids, 0, windows, 0, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_NUM_WINDOWS);

windows[0] = -1;
ret = tsk_treeseq_divergence_matrix(&ts, 2, sample_ids, 2, windows, 0, result);
ret = tsk_treeseq_divergence_matrix(&ts, 2, NULL, sample_ids, 2, windows, 0, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_WINDOWS);

windows[0] = 0.45;
windows[2] = 1.5;
ret = tsk_treeseq_divergence_matrix(&ts, 2, sample_ids, 2, windows, 0, result);
ret = tsk_treeseq_divergence_matrix(&ts, 2, NULL, sample_ids, 2, windows, 0, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_WINDOWS);

windows[0] = 0.55;
windows[2] = 1.0;
ret = tsk_treeseq_divergence_matrix(&ts, 2, sample_ids, 2, windows, 0, result);
ret = tsk_treeseq_divergence_matrix(&ts, 2, NULL, sample_ids, 2, windows, 0, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_WINDOWS);

tsk_treeseq_free(&ts);
Expand All @@ -2558,7 +2616,7 @@ test_simplest_divergence_matrix_internal_sample(void)
{
const char *nodes = "1 0 0\n"
"1 0 0\n"
"0 1 0\n";
"1 1 0\n";
const char *edges = "0 1 2 0,1\n";
tsk_treeseq_t ts;
tsk_id_t sample_ids[] = { 0, 1, 2 };
Expand All @@ -2570,12 +2628,12 @@ test_simplest_divergence_matrix_internal_sample(void)
tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, NULL, NULL, NULL, NULL, 0);

ret = tsk_treeseq_divergence_matrix(
&ts, 3, sample_ids, 0, NULL, TSK_STAT_BRANCH, result);
&ts, 3, NULL, sample_ids, 0, NULL, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(9, D_branch, result);

ret = tsk_treeseq_divergence_matrix(
&ts, 3, sample_ids, 0, NULL, TSK_STAT_SITE, result);
&ts, 3, NULL, sample_ids, 0, NULL, TSK_STAT_SITE, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);
assert_arrays_almost_equal(9, D_site, result);

Expand Down
5 changes: 3 additions & 2 deletions c/tests/test_trees.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8008,9 +8008,10 @@ test_time_uncalibrated(void)
TSK_STAT_BRANCH | TSK_STAT_ALLOW_TIME_UNCALIBRATED, sigma);
CU_ASSERT_EQUAL_FATAL(ret, 0);

ret = tsk_treeseq_divergence_matrix(&ts2, 0, NULL, 0, NULL, TSK_STAT_BRANCH, result);
ret = tsk_treeseq_divergence_matrix(
&ts2, 0, NULL, NULL, 0, NULL, TSK_STAT_BRANCH, result);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_TIME_UNCALIBRATED);
ret = tsk_treeseq_divergence_matrix(&ts2, 0, NULL, 0, NULL,
ret = tsk_treeseq_divergence_matrix(&ts2, 0, NULL, NULL, 0, NULL,
TSK_STAT_BRANCH | TSK_STAT_ALLOW_TIME_UNCALIBRATED, result);
CU_ASSERT_EQUAL_FATAL(ret, 0);

Expand Down
10 changes: 0 additions & 10 deletions c/tests/testlib.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -966,16 +966,6 @@ tskit_suite_init(void)
return CUE_SUCCESS;
}

void
assert_arrays_almost_equal(tsk_size_t len, double *a, double *b)
{
tsk_size_t j;

for (j = 0; j < len; j++) {
CU_ASSERT_DOUBLE_EQUAL(a[j], b[j], 1e-9);
}
}

static int
tskit_suite_cleanup(void)
{
Expand Down
11 changes: 10 additions & 1 deletion c/tests/testlib.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,16 @@ void parse_individuals(const char *text, tsk_individual_table_t *individual_tabl

void unsort_edges(tsk_edge_table_t *edges, size_t start);

void assert_arrays_almost_equal(tsk_size_t len, double *a, double *b);
/* Use a macro so we can get line numbers at roughly the right place */
#define assert_arrays_almost_equal(len, a, b) \
{ \
do { \
tsk_size_t _j; \
for (_j = 0; _j < len; _j++) { \
CU_ASSERT_DOUBLE_EQUAL(a[_j], b[_j], 1e-9); \
} \
} while (0); \
}

extern const char *single_tree_ex_nodes;
extern const char *single_tree_ex_edges;
Expand Down
Loading