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Change order of output dims; use summary function in pair_coalescence…
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@nspope @mergify
nspope authored and mergify[bot] committed Aug 7, 2024
1 parent 1f28c11 commit 0403de0
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Showing 10 changed files with 270 additions and 171 deletions.
66 changes: 39 additions & 27 deletions c/tests/test_stats.c
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Original file line number Diff line number Diff line change
Expand Up @@ -319,9 +319,9 @@ verify_pair_coalescence_counts(tsk_treeseq_t *ts, tsk_flags_t options)
tsk_id_t sample_sets[n];
tsk_size_t sample_set_sizes[P];
tsk_id_t index_tuples[2 * I];
tsk_id_t node_output_map[N];
tsk_id_t node_bin_map[N];
tsk_size_t dim = T * N * I;
double C1[dim];
double C[dim];
tsk_size_t i, j, k;

for (i = 0; i < n; i++) {
Expand All @@ -343,53 +343,67 @@ verify_pair_coalescence_counts(tsk_treeseq_t *ts, tsk_flags_t options)
}
}

/* test various bin assignments */
for (i = 0; i < N; i++) {
node_output_map[i] = (tsk_id_t) i;
node_bin_map[i] = ((tsk_id_t) i) % 8;
}
ret = tsk_treeseq_pair_coalescence_counts(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, T, breakpoints, 8, node_bin_map, options, C);
CU_ASSERT_EQUAL_FATAL(ret, 0);

ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, T, breakpoints, N, node_output_map, options, C1);
for (i = 0; i < N; i++) {
node_bin_map[i] = i < N / 2 ? ((tsk_id_t) i) : TSK_NULL;
}
ret = tsk_treeseq_pair_coalescence_counts(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, T, breakpoints, N / 2, node_bin_map, options, C);
CU_ASSERT_EQUAL_FATAL(ret, 0);

for (i = 0; i < N; i++) {
node_bin_map[i] = (tsk_id_t) i;
}
ret = tsk_treeseq_pair_coalescence_counts(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, T, breakpoints, N, node_bin_map, options, C);
CU_ASSERT_EQUAL_FATAL(ret, 0);
/* TODO: test against naive pairs per node per tree */
/* TODO: compare against naive pairs per node per tree */

/* cover errors */
double bad_breakpoints[2] = { breakpoints[1], 0.0 };
ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, 1, bad_breakpoints, N, node_output_map, options, C1);
ret = tsk_treeseq_pair_coalescence_counts(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, 1, bad_breakpoints, N, node_bin_map, options, C);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_WINDOWS);

index_tuples[0] = (tsk_id_t) P;
ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, 1, breakpoints, N, node_output_map, options, C1);
ret = tsk_treeseq_pair_coalescence_counts(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, 1, breakpoints, N, node_bin_map, options, C);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_SAMPLE_SET_INDEX);
index_tuples[0] = 0;

tsk_size_t tmp = sample_set_sizes[0];
sample_set_sizes[0] = 0;
ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, 1, breakpoints, N, node_output_map, options, C1);
ret = tsk_treeseq_pair_coalescence_counts(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, 1, breakpoints, N, node_bin_map, options, C);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_EMPTY_SAMPLE_SET);
sample_set_sizes[0] = tmp;

sample_sets[1] = 0;
ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, 1, breakpoints, N, node_output_map, options, C1);
ret = tsk_treeseq_pair_coalescence_counts(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, 1, breakpoints, N, node_bin_map, options, C);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_DUPLICATE_SAMPLE);
sample_sets[1] = 1;

ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, 1, breakpoints, N - 1, node_output_map, options, C1);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_NODE_OUTPUT_MAP_DIM);
ret = tsk_treeseq_pair_coalescence_counts(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, 1, breakpoints, N - 1, node_bin_map, options, C);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_NODE_BIN_MAP_DIM);

ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, 1, breakpoints, 0, node_output_map, options, C1);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_NODE_OUTPUT_MAP_DIM);
ret = tsk_treeseq_pair_coalescence_counts(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, 1, breakpoints, 0, node_bin_map, options, C);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_NODE_BIN_MAP_DIM);

node_output_map[0] = -2;
ret = tsk_treeseq_pair_coalescence_stat(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, 1, breakpoints, N, node_output_map, options, C1);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_NODE_OUTPUT_MAP);
node_output_map[0] = 0;
node_bin_map[0] = -2;
ret = tsk_treeseq_pair_coalescence_counts(ts, P, sample_set_sizes, sample_sets, I,
index_tuples, 1, breakpoints, N, node_bin_map, options, C);
CU_ASSERT_EQUAL_FATAL(ret, TSK_ERR_BAD_NODE_BIN_MAP);
node_bin_map[0] = 0;
}

typedef struct {
Expand Down Expand Up @@ -2880,8 +2894,6 @@ test_pair_coalescence_counts(void)
tsk_treeseq_t ts;
tsk_treeseq_from_text(&ts, 100, nonbinary_ex_nodes, nonbinary_ex_edges, NULL,
nonbinary_ex_sites, nonbinary_ex_mutations, NULL, NULL, 0);
verify_pair_coalescence_counts(&ts, TSK_STAT_NODE);
verify_pair_coalescence_counts(&ts, TSK_STAT_NODE | TSK_STAT_SPAN_NORMALISE);
verify_pair_coalescence_counts(&ts, 0);
verify_pair_coalescence_counts(&ts, TSK_STAT_SPAN_NORMALISE);
tsk_treeseq_free(&ts);
Expand Down
14 changes: 8 additions & 6 deletions c/tskit/core.c
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Original file line number Diff line number Diff line change
Expand Up @@ -484,13 +484,15 @@ tsk_strerror_internal(int err)
ret = "Insufficient weights provided (at least 1 required). "
"(TSK_ERR_INSUFFICIENT_WEIGHTS)";
break;
case TSK_ERR_BAD_NODE_OUTPUT_MAP:
ret = "Node output map contains values less than TSK_NULL. "
"(TSK_ERR_BAD_NODE_OUTPUT_MAP)";

/* Pair coalescence errors */
case TSK_ERR_BAD_NODE_BIN_MAP:
ret = "Node-to-bin map contains values less than TSK_NULL. "
"(TSK_ERR_BAD_NODE_BIN_MAP)";
break;
case TSK_ERR_BAD_NODE_OUTPUT_MAP_DIM:
ret = "Maximum index in node output map does not match "
"output dimension. (TSK_ERR_BAD_NODE_OUTPUT_MAP_DIM)";
case TSK_ERR_BAD_NODE_BIN_MAP_DIM:
ret = "Maximum index in node-to-bin map does not match "
"output dimension. (TSK_ERR_BAD_NODE_BIN_MAP_DIM)";
break;

/* Mutation mapping errors */
Expand Down
8 changes: 4 additions & 4 deletions c/tskit/core.h
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Original file line number Diff line number Diff line change
Expand Up @@ -695,13 +695,13 @@ Insufficient weights were provided.
*/
#define TSK_ERR_INSUFFICIENT_WEIGHTS -913
/**
The node output map contains a value less than TSK_NULL.
The node bin map contains a value less than TSK_NULL.
*/
#define TSK_ERR_BAD_NODE_OUTPUT_MAP -914
#define TSK_ERR_BAD_NODE_BIN_MAP -914
/**
Maximum index in node output map does not match output dimension.
Maximum index in node bin map does not match output dimension.
*/
#define TSK_ERR_BAD_NODE_OUTPUT_MAP_DIM -915
#define TSK_ERR_BAD_NODE_BIN_MAP_DIM -915
/** @} */

/**
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