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Two locus general matrix #3426

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cc2612f
initial stab at a general matrix (no normalisation)
lkirk Oct 26, 2025
d53a662
added dimension dropping, but I think transposing is better -- we don…
lkirk Oct 26, 2025
ea30828
finalize and add tests for single and multipop
lkirk Dec 4, 2025
cef7149
reformat jitter
lkirk Dec 4, 2025
08e4d3f
one more reformat jitter
lkirk Dec 4, 2025
7f5c1c4
one more one more reformat jitter
lkirk Dec 4, 2025
904a809
turns out, the general norm function needs to know the state_dims
lkirk Dec 4, 2025
688792c
fix up a bit of naming in general test funcs, remove unneeded branch,…
lkirk Dec 4, 2025
baebca6
flake8 does not like assigning lambdas to variables
lkirk Dec 4, 2025
a260cf0
and black doesn't like that
lkirk Dec 4, 2025
46a4e19
do not test equality, this was useful on my local machine but is prob…
lkirk Dec 7, 2025
209e554
formatting jitter
lkirk Mar 6, 2026
3a8944f
lowlevel tests
lkirk Mar 9, 2026
b41239a
relax diff requirements (macos failure)
lkirk Mar 9, 2026
c9e1df1
relax diff requirements (macos failure) -- previous commit fixed one
lkirk Mar 9, 2026
51ec346
new formatting tools, fix lint
lkirk Mar 9, 2026
e5a105f
remove TODOs, old comment and tested elsewhere
lkirk Mar 10, 2026
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79 changes: 46 additions & 33 deletions c/tskit/trees.c
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2298,8 +2298,9 @@ get_allele_samples(const tsk_site_t *site, tsk_size_t site_offset,
}

static int
norm_hap_weighted(tsk_size_t result_dim, const double *hap_weights,
tsk_size_t TSK_UNUSED(n_a), tsk_size_t TSK_UNUSED(n_b), double *result, void *params)
norm_hap_weighted(tsk_size_t TSK_UNUSED(state_dim), const double *hap_weights,
tsk_size_t result_dim, tsk_size_t TSK_UNUSED(n_a), tsk_size_t TSK_UNUSED(n_b),
double *result, void *params)
{
sample_count_stat_params_t args = *(sample_count_stat_params_t *) params;
const double *weight_row;
Expand All @@ -2315,8 +2316,9 @@ norm_hap_weighted(tsk_size_t result_dim, const double *hap_weights,
}

static int
norm_hap_weighted_ij(tsk_size_t result_dim, const double *hap_weights,
tsk_size_t TSK_UNUSED(n_a), tsk_size_t TSK_UNUSED(n_b), double *result, void *params)
norm_hap_weighted_ij(tsk_size_t TSK_UNUSED(state_dim), const double *hap_weights,
tsk_size_t result_dim, tsk_size_t TSK_UNUSED(n_a), tsk_size_t TSK_UNUSED(n_b),
double *result, void *params)
{
sample_count_stat_params_t args = *(sample_count_stat_params_t *) params;
const double *weight_row;
Expand All @@ -2341,8 +2343,9 @@ norm_hap_weighted_ij(tsk_size_t result_dim, const double *hap_weights,
}

static int
norm_total_weighted(tsk_size_t result_dim, const double *TSK_UNUSED(hap_weights),
tsk_size_t n_a, tsk_size_t n_b, double *result, void *TSK_UNUSED(params))
norm_total_weighted(tsk_size_t TSK_UNUSED(state_dim),
const double *TSK_UNUSED(hap_weights), tsk_size_t result_dim, tsk_size_t n_a,
tsk_size_t n_b, double *result, void *TSK_UNUSED(params))
{
tsk_size_t k;
double norm = 1 / (double) (n_a * n_b);
Expand Down Expand Up @@ -2411,8 +2414,8 @@ static int
compute_general_normed_two_site_stat_result(const tsk_bitset_t *state,
const tsk_size_t *allele_counts, tsk_size_t a_off, tsk_size_t b_off,
tsk_size_t num_a_alleles, tsk_size_t num_b_alleles, tsk_size_t state_dim,
tsk_size_t result_dim, general_stat_func_t *f, sample_count_stat_params_t *f_params,
norm_func_t *norm_f, bool polarised, two_locus_work_t *restrict work, double *result)
tsk_size_t result_dim, general_stat_func_t *f, void *f_params, norm_func_t *norm_f,
bool polarised, two_locus_work_t *restrict work, double *result)
{
int ret = 0;
// Sample sets and b sites are rows, a sites are columns
Expand Down Expand Up @@ -2445,7 +2448,7 @@ compute_general_normed_two_site_stat_result(const tsk_bitset_t *state,
if (ret != 0) {
goto out;
}
ret = norm_f(result_dim, weights, num_a_alleles - is_polarised,
ret = norm_f(state_dim, weights, result_dim, num_a_alleles - is_polarised,
num_b_alleles - is_polarised, norm, f_params);
if (ret != 0) {
goto out;
Expand All @@ -2463,9 +2466,8 @@ compute_general_normed_two_site_stat_result(const tsk_bitset_t *state,
static int
compute_general_two_site_stat_result(const tsk_bitset_t *state,
const tsk_size_t *allele_counts, tsk_size_t a_off, tsk_size_t b_off,
tsk_size_t state_dim, tsk_size_t result_dim, general_stat_func_t *f,
sample_count_stat_params_t *f_params, two_locus_work_t *restrict work,
double *result)
tsk_size_t state_dim, tsk_size_t result_dim, general_stat_func_t *f, void *f_params,
two_locus_work_t *restrict work, double *result)
{
int ret = 0;
tsk_size_t k;
Expand Down Expand Up @@ -2653,9 +2655,8 @@ static int
tsk_treeseq_two_site_count_stat(const tsk_treeseq_t *self, tsk_size_t state_dim,
tsk_size_t num_sample_sets, const tsk_size_t *sample_set_sizes,
const tsk_id_t *sample_sets, tsk_size_t result_dim, general_stat_func_t *f,
sample_count_stat_params_t *f_params, norm_func_t *norm_f, tsk_size_t n_rows,
const tsk_id_t *row_sites, tsk_size_t n_cols, const tsk_id_t *col_sites,
tsk_flags_t options, double *result)
void *f_params, norm_func_t *norm_f, tsk_size_t n_rows, const tsk_id_t *row_sites,
tsk_size_t n_cols, const tsk_id_t *col_sites, tsk_flags_t options, double *result)
{
int ret = 0;
tsk_bitset_t allele_samples, allele_sample_sets;
Expand Down Expand Up @@ -3089,9 +3090,8 @@ advance_collect_edges(iter_state *s, tsk_id_t index)
static int
compute_two_tree_branch_state_update(const tsk_treeseq_t *ts, tsk_id_t c,
const iter_state *A_state, const iter_state *B_state, tsk_size_t state_dim,
tsk_size_t result_dim, int sign, general_stat_func_t *f,
sample_count_stat_params_t *f_params, two_locus_work_t *restrict work,
double *result)
tsk_size_t result_dim, int sign, general_stat_func_t *f, void *f_params,
two_locus_work_t *restrict work, double *result)
{
int ret = 0;
double a_len, b_len;
Expand Down Expand Up @@ -3141,8 +3141,8 @@ compute_two_tree_branch_state_update(const tsk_treeseq_t *ts, tsk_id_t c,

static int
compute_two_tree_branch_stat(const tsk_treeseq_t *ts, const iter_state *l_state,
iter_state *r_state, general_stat_func_t *f, sample_count_stat_params_t *f_params,
tsk_size_t result_dim, tsk_size_t state_dim, double *result)
iter_state *r_state, general_stat_func_t *f, void *f_params, tsk_size_t result_dim,
tsk_size_t state_dim, double *result)
{
int ret = 0;
tsk_id_t e, c, ec, p, *updated_nodes = NULL;
Expand Down Expand Up @@ -3243,9 +3243,9 @@ static int
tsk_treeseq_two_branch_count_stat(const tsk_treeseq_t *self, tsk_size_t state_dim,
tsk_size_t num_sample_sets, const tsk_size_t *sample_set_sizes,
const tsk_id_t *sample_sets, tsk_size_t result_dim, general_stat_func_t *f,
sample_count_stat_params_t *f_params, norm_func_t *TSK_UNUSED(norm_f),
tsk_size_t n_rows, const double *row_positions, tsk_size_t n_cols,
const double *col_positions, tsk_flags_t TSK_UNUSED(options), double *result)
void *f_params, norm_func_t *TSK_UNUSED(norm_f), tsk_size_t n_rows,
const double *row_positions, tsk_size_t n_cols, const double *col_positions,
tsk_flags_t TSK_UNUSED(options), double *result)
{
int ret = 0;
int r, c;
Expand Down Expand Up @@ -3385,10 +3385,10 @@ check_sample_set_dups(tsk_size_t num_sample_sets, const tsk_size_t *sample_set_s
}

int
tsk_treeseq_two_locus_count_stat(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
tsk_size_t result_dim, const tsk_id_t *set_indexes, general_stat_func_t *f,
norm_func_t *norm_f, tsk_size_t out_rows, const tsk_id_t *row_sites,
tsk_treeseq_two_locus_count_general_stat(const tsk_treeseq_t *self,
tsk_size_t num_sample_sets, const tsk_size_t *sample_set_sizes,
const tsk_id_t *sample_sets, tsk_size_t result_dim, general_stat_func_t *f,
void *f_params, norm_func_t *norm_f, tsk_size_t out_rows, const tsk_id_t *row_sites,
const double *row_positions, tsk_size_t out_cols, const tsk_id_t *col_sites,
const double *col_positions, tsk_flags_t options, double *result)
{
Expand All @@ -3398,10 +3398,6 @@ tsk_treeseq_two_locus_count_stat(const tsk_treeseq_t *self, tsk_size_t num_sampl
bool stat_site = !!(options & TSK_STAT_SITE);
bool stat_branch = !!(options & TSK_STAT_BRANCH);
tsk_size_t state_dim = num_sample_sets;
sample_count_stat_params_t f_params = { .sample_sets = sample_sets,
.num_sample_sets = num_sample_sets,
.sample_set_sizes = sample_set_sizes,
.set_indexes = set_indexes };

// We do not support two-locus node stats
if (!!(options & TSK_STAT_NODE)) {
Expand Down Expand Up @@ -3441,7 +3437,7 @@ tsk_treeseq_two_locus_count_stat(const tsk_treeseq_t *self, tsk_size_t num_sampl
goto out;
}
ret = tsk_treeseq_two_site_count_stat(self, state_dim, num_sample_sets,
sample_set_sizes, sample_sets, result_dim, f, &f_params, norm_f, out_rows,
sample_set_sizes, sample_sets, result_dim, f, f_params, norm_f, out_rows,
row_sites, out_cols, col_sites, options, result);
} else if (stat_branch) {
ret = check_positions(
Expand All @@ -3455,13 +3451,30 @@ tsk_treeseq_two_locus_count_stat(const tsk_treeseq_t *self, tsk_size_t num_sampl
goto out;
}
ret = tsk_treeseq_two_branch_count_stat(self, state_dim, num_sample_sets,
sample_set_sizes, sample_sets, result_dim, f, &f_params, norm_f, out_rows,
sample_set_sizes, sample_sets, result_dim, f, f_params, norm_f, out_rows,
row_positions, out_cols, col_positions, options, result);
}
out:
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@petrelharp petrelharp Mar 14, 2026

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I don't know why codecov says this line is not covered; do you? (sticking some prints or asserts in here can help track that down)

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@lkirk lkirk Mar 14, 2026

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Judging from the coverage of the rest of that function (every goto being hit), my best guess is that the compiler is optimizing that label out. In fact, I could just change all of those goto ret to return ret and remove the out: label since we're not doing any sort of cleanup at the end of this function.

return ret;
}

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@lkirk lkirk Mar 10, 2026

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This function now serves as an inner wrapper. The the general stat accepts the summary function params so that the CPython code can pass them directly. All of the specialized stats functions call this function.

int
tsk_treeseq_two_locus_count_stat(const tsk_treeseq_t *self, tsk_size_t num_sample_sets,
const tsk_size_t *sample_set_sizes, const tsk_id_t *sample_sets,
tsk_size_t result_dim, const tsk_id_t *set_indexes, general_stat_func_t *f,
norm_func_t *norm_f, tsk_size_t out_rows, const tsk_id_t *row_sites,
const double *row_positions, tsk_size_t out_cols, const tsk_id_t *col_sites,
const double *col_positions, tsk_flags_t options, double *result)
{
sample_count_stat_params_t f_params = { .sample_sets = sample_sets,
.num_sample_sets = num_sample_sets,
.sample_set_sizes = sample_set_sizes,
.set_indexes = set_indexes };
return tsk_treeseq_two_locus_count_general_stat(self, num_sample_sets,
sample_set_sizes, sample_sets, result_dim, f, &f_params, norm_f, out_rows,
row_sites, row_positions, out_cols, col_sites, col_positions, options, result);
}

/***********************************
* Allele frequency spectrum
***********************************/
Expand Down
11 changes: 9 additions & 2 deletions c/tskit/trees.h
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Original file line number Diff line number Diff line change
Expand Up @@ -1036,8 +1036,8 @@ int tsk_treeseq_general_stat(const tsk_treeseq_t *self, tsk_size_t K, const doub
tsk_size_t M, general_stat_func_t *f, void *f_params, tsk_size_t num_windows,
const double *windows, tsk_flags_t options, double *result);

typedef int norm_func_t(tsk_size_t result_dim, const double *hap_weights, tsk_size_t n_a,
tsk_size_t n_b, double *result, void *params);
typedef int norm_func_t(tsk_size_t state_dim, const double *hap_weights,
tsk_size_t result_dim, tsk_size_t n_a, tsk_size_t n_b, double *result, void *params);

int tsk_treeseq_two_locus_count_stat(const tsk_treeseq_t *self,
tsk_size_t num_sample_sets, const tsk_size_t *sample_set_sizes,
Expand Down Expand Up @@ -1120,6 +1120,13 @@ typedef int general_sample_stat_method(const tsk_treeseq_t *self,
const tsk_id_t *sample_sets, tsk_size_t num_indexes, const tsk_id_t *indexes,
tsk_size_t num_windows, const double *windows, tsk_flags_t options, double *result);

int tsk_treeseq_two_locus_count_general_stat(const tsk_treeseq_t *self,
tsk_size_t num_sample_sets, const tsk_size_t *sample_set_sizes,
const tsk_id_t *sample_sets, tsk_size_t result_dim, general_stat_func_t *f,
void *f_params, norm_func_t *norm_f, tsk_size_t out_rows, const tsk_id_t *row_sites,
const double *row_positions, tsk_size_t out_cols, const tsk_id_t *col_sites,
const double *col_positions, tsk_flags_t options, double *result);

typedef int two_locus_count_stat_method(const tsk_treeseq_t *self,
tsk_size_t num_sample_sets, const tsk_size_t *sample_set_sizes,
const tsk_id_t *sample_sets, tsk_size_t num_rows, const tsk_id_t *row_sites,
Expand Down
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