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allow genetic_relatedness_vector to do windows that don't span the whole genome #3003

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Sep 27, 2024
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allow genetic_relatedness_vector to do windows that don't span the whole genome #3003

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b30c669
Allow windows for genetic_relatedness_vector to not span the whole
petrelharp Sep 25, 2024
39e8145
allow genetic_relatedness_vector to work with arbitrary nodes; closes…
petrelharp Sep 27, 2024
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103 changes: 83 additions & 20 deletions c/tests/test_stats.c
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Original file line number Diff line number Diff line change
Expand Up @@ -2017,11 +2017,17 @@ test_empty_genetic_relatedness_vector(void)
}

ret = tsk_treeseq_genetic_relatedness_vector(
&ts, num_weights, weights, 1, windows, result, 0);
&ts, num_weights, weights, 1, windows, num_samples, ts.samples, result, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

ret = tsk_treeseq_genetic_relatedness_vector(&ts, num_weights, weights, 1, windows,
num_samples, ts.samples, result, TSK_STAT_NONCENTRED);
CU_ASSERT_EQUAL_FATAL(ret, 0);

windows[0] = 0.5 * tsk_treeseq_get_sequence_length(&ts);
windows[1] = 0.75 * tsk_treeseq_get_sequence_length(&ts);
ret = tsk_treeseq_genetic_relatedness_vector(
&ts, num_weights, weights, 1, windows, result, TSK_STAT_NONCENTRED);
&ts, num_weights, weights, 1, windows, num_samples, ts.samples, result, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

tsk_treeseq_free(&ts);
Expand Down Expand Up @@ -2055,17 +2061,26 @@ verify_genetic_relatedness_vector(
}
}

ret = tsk_treeseq_genetic_relatedness_vector(
ts, num_weights, weights, num_windows, windows, result, 0);
ret = tsk_treeseq_genetic_relatedness_vector(ts, num_weights, weights, num_windows,
windows, num_samples, ts->samples, result, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

ret = tsk_treeseq_genetic_relatedness_vector(
ts, num_weights, weights, num_windows, windows, result, TSK_STAT_NONCENTRED);
windows[0] = windows[1] / 2;
if (num_windows > 1) {
windows[num_windows - 1]
= windows[num_windows - 2] + (L / (double) (2 * num_windows));
}
ret = tsk_treeseq_genetic_relatedness_vector(ts, num_weights, weights, num_windows,
windows, num_samples, ts->samples, result, 0);
CU_ASSERT_EQUAL_FATAL(ret, 0);

ret = tsk_treeseq_genetic_relatedness_vector(ts, num_weights, weights, num_windows,
windows, num_samples, ts->samples, result, TSK_STAT_NONCENTRED);
CU_ASSERT_EQUAL_FATAL(ret, 0);

tsk_set_debug_stream(_devnull);
ret = tsk_treeseq_genetic_relatedness_vector(
ts, num_weights, weights, num_windows, windows, result, TSK_DEBUG);
ret = tsk_treeseq_genetic_relatedness_vector(ts, num_weights, weights, num_windows,
windows, num_samples, ts->samples, result, TSK_DEBUG);
CU_ASSERT_EQUAL_FATAL(ret, 0);
tsk_set_debug_stream(stdout);

Expand Down Expand Up @@ -2102,6 +2117,7 @@ test_paper_ex_genetic_relatedness_vector_errors(void)
tsk_size_t num_samples;
double *weights, *result;
tsk_size_t j;
tsk_size_t num_windows = 2;
tsk_size_t num_weights = 2;
double windows[] = { 0, 0, 0 };

Expand All @@ -2110,7 +2126,7 @@ test_paper_ex_genetic_relatedness_vector_errors(void)
num_samples = tsk_treeseq_get_num_samples(&ts);

weights = tsk_malloc(num_weights * num_samples * sizeof(double));
result = tsk_malloc(num_weights * num_samples * sizeof(double));
result = tsk_malloc(num_windows * num_weights * num_samples * sizeof(double));
for (j = 0; j < num_samples; j++) {
weights[j] = 1.0;
}
Expand All @@ -2120,48 +2136,93 @@ test_paper_ex_genetic_relatedness_vector_errors(void)

/* Window errors */
ret = tsk_treeseq_genetic_relatedness_vector(
&ts, 1, weights, 0, windows, result, TSK_STAT_BRANCH);
&ts, 1, weights, 0, windows, num_samples, ts.samples, result, TSK_STAT_BRANCH);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_NUM_WINDOWS);
ret = tsk_treeseq_genetic_relatedness_vector(
&ts, 1, weights, 0, NULL, result, TSK_STAT_BRANCH);
&ts, 1, weights, 0, NULL, num_samples, ts.samples, result, TSK_STAT_BRANCH);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_NUM_WINDOWS);

ret = tsk_treeseq_genetic_relatedness_vector(
&ts, 1, weights, 2, windows, result, TSK_STAT_BRANCH);
&ts, 1, weights, 2, windows, num_samples, ts.samples, result, TSK_STAT_BRANCH);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_WINDOWS);

windows[0] = -1;
ret = tsk_treeseq_genetic_relatedness_vector(
&ts, 1, weights, 2, windows, result, TSK_STAT_BRANCH);
&ts, 1, weights, 2, windows, num_samples, ts.samples, result, TSK_STAT_BRANCH);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_WINDOWS);

windows[0] = 10;
windows[0] = 12;
ret = tsk_treeseq_genetic_relatedness_vector(
&ts, 1, weights, 2, windows, result, TSK_STAT_BRANCH);
&ts, 1, weights, 2, windows, num_samples, ts.samples, result, TSK_STAT_BRANCH);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_WINDOWS);

windows[0] = 0;
windows[2] = 12;
ret = tsk_treeseq_genetic_relatedness_vector(
&ts, 1, weights, 2, windows, result, TSK_STAT_BRANCH);
&ts, 1, weights, 2, windows, num_samples, ts.samples, result, TSK_STAT_BRANCH);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_WINDOWS);

/* unsupported mode errors */
windows[0] = 0.0;
windows[1] = 5.0;
windows[2] = 10.0;
ret = tsk_treeseq_genetic_relatedness_vector(
&ts, num_weights, weights, 2, windows, result, TSK_STAT_SITE);
ret = tsk_treeseq_genetic_relatedness_vector(&ts, num_weights, weights, 2, windows,
num_samples, ts.samples, result, TSK_STAT_SITE);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_UNSUPPORTED_STAT_MODE);
ret = tsk_treeseq_genetic_relatedness_vector(
&ts, num_weights, weights, 2, windows, result, TSK_STAT_NODE);
ret = tsk_treeseq_genetic_relatedness_vector(&ts, num_weights, weights, 2, windows,
num_samples, ts.samples, result, TSK_STAT_NODE);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_UNSUPPORTED_STAT_MODE);

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

static void
test_paper_ex_genetic_relatedness_vector_node_errors(void)
{
int ret;
tsk_treeseq_t ts;
tsk_size_t num_samples;
double *weights, *result;
tsk_size_t j;
tsk_size_t num_weights = 2;
tsk_size_t num_windows = 2;
double windows[] = { 1, 1.5, 2 };
tsk_size_t num_nodes = 3;
const tsk_id_t good_nodes[] = { 1, 0, 2 };
const tsk_id_t bad_nodes1[] = { 1, -1, 2 };
const tsk_id_t bad_nodes2[] = { 1, 100, 2 };

tsk_treeseq_from_text(&ts, 10, paper_ex_nodes, paper_ex_edges, NULL, paper_ex_sites,
paper_ex_mutations, paper_ex_individuals, NULL, 0);
num_samples = tsk_treeseq_get_num_samples(&ts);

weights = tsk_malloc(num_weights * num_samples * sizeof(double));
result = tsk_malloc(num_windows * num_weights * num_nodes * sizeof(double));
for (j = 0; j < num_samples; j++) {
weights[j] = 1.0;
}
for (j = 0; j < num_samples; j++) {
weights[j + num_samples] = (float) j;
}

/* node errors */
ret = tsk_treeseq_genetic_relatedness_vector(&ts, num_weights, weights, 2, windows,
num_nodes, good_nodes, result, TSK_STAT_BRANCH);
CU_ASSERT_EQUAL_FATAL(ret, 0);
ret = tsk_treeseq_genetic_relatedness_vector(&ts, num_weights, weights, 2, windows,
num_nodes, bad_nodes1, result, TSK_STAT_BRANCH);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_NODE_OUT_OF_BOUNDS);
ret = tsk_treeseq_genetic_relatedness_vector(&ts, num_weights, weights, 2, windows,
num_nodes, bad_nodes2, result, TSK_STAT_BRANCH);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_NODE_OUT_OF_BOUNDS);

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

static void
test_paper_ex_Y2_errors(void)
{
Expand Down Expand Up @@ -3708,6 +3769,8 @@ main(int argc, char **argv)
test_paper_ex_genetic_relatedness_vector },
{ "test_paper_ex_genetic_relatedness_vector_errors",
test_paper_ex_genetic_relatedness_vector_errors },
{ "test_paper_ex_genetic_relatedness_vector_node_errors",
test_paper_ex_genetic_relatedness_vector_node_errors },
{ "test_paper_ex_Y2_errors", test_paper_ex_Y2_errors },
{ "test_paper_ex_Y2", test_paper_ex_Y2 },
{ "test_paper_ex_f2_errors", test_paper_ex_f2_errors },
Expand Down
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