Skip to content

Commit

Permalink
Address PR comments
Browse files Browse the repository at this point in the history 
Move memset calls to be after declarations

self->tree in get_mutation_samples

minor issues
  • Loading branch information
@lkirk
lkirk committed Aug 29, 2023
1 parent 50a0144 commit aafb78f
Showing 1 changed file with 21 additions and 22 deletions.
43 changes: 21 additions & 22 deletions c/tskit/trees.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2205,16 +2205,15 @@ get_allele_samples(const tsk_site_t *site, const tsk_bit_array_t *state,
}

static int
get_mutation_samples(const tsk_tree_t *self, const tsk_size_t *site_offsets,
get_mutation_samples(const tsk_tree_t *tree, const tsk_size_t *site_offsets,
tsk_bit_array_t *allele_samples, tsk_size_t **num_alleles)
{
int ret = 0;

const tsk_treeseq_t *restrict ts = self->tree_sequence;
const tsk_treeseq_t *restrict ts = tree->tree_sequence;

const tsk_size_t num_samples = tsk_treeseq_get_num_samples(ts);
const tsk_size_t num_tree_sites = ts->tree_sites_length[self->index];
const tsk_site_t *restrict tree_sites = ts->tree_sites[self->index];
const tsk_site_t *restrict tree_sites = ts->tree_sites[tree->index];
const tsk_flags_t *restrict flags = ts->tables->nodes.flags;
const tsk_id_t *restrict mut_nodes = ts->tables->mutations.node;

Expand All @@ -2224,11 +2223,11 @@ get_mutation_samples(const tsk_tree_t *self, const tsk_size_t *site_offsets,
tsk_size_t num_mutations, mut_samples_offset, mut_offset;
tsk_size_t s, m, n;

tsk_memset(&mut_samples, 0, sizeof(mut_samples));

tsk_id_t node;
tsk_size_t num_nodes;
tsk_id_t *nodes = tsk_malloc(tsk_tree_get_size_bound(self) * sizeof(*nodes));
tsk_id_t *nodes = tsk_malloc(tsk_tree_get_size_bound(tree) * sizeof(*nodes));

tsk_memset(&mut_samples, 0, sizeof(mut_samples));

if (nodes == NULL) {
ret = TSK_ERR_NO_MEMORY;
Expand All @@ -2237,9 +2236,8 @@ get_mutation_samples(const tsk_tree_t *self, const tsk_size_t *site_offsets,

// Get the number of mutations
num_mutations = 0;
for (s = 0; s < num_tree_sites; s++) {
site = &tree_sites[s];
num_mutations += site->mutations_length;
for (s = 0; s < tree->sites_length; s++) {
num_mutations += tree_sites[s].mutations_length;
}

ret = tsk_bit_array_init(&mut_samples, num_samples, num_mutations);
Expand All @@ -2248,7 +2246,7 @@ get_mutation_samples(const tsk_tree_t *self, const tsk_size_t *site_offsets,
}

// Current position minus num ancestral alleles to this point, if there are any sites
mut_offset = num_tree_sites
mut_offset = tree->sites_length
? (site_offsets[tree_sites[0].id] - (tsk_size_t) tree_sites[0].id)
: 0;

Expand All @@ -2259,7 +2257,7 @@ get_mutation_samples(const tsk_tree_t *self, const tsk_size_t *site_offsets,
for (m = 0; m < num_mutations; m++) {
tsk_bit_array_get_row(&mut_samples, m, &mut_samples_row);

ret = tsk_tree_preorder_from(self, mut_nodes[m + mut_offset], nodes, &num_nodes);
ret = tsk_tree_preorder_from(tree, mut_nodes[m + mut_offset], nodes, &num_nodes);
if (ret != 0) {
goto out;
}
Expand All @@ -2273,7 +2271,7 @@ get_mutation_samples(const tsk_tree_t *self, const tsk_size_t *site_offsets,
}

mut_samples_offset = 0;
for (s = 0; s < num_tree_sites; s++) {
for (s = 0; s < tree->sites_length; s++) {
site = &tree_sites[s];

tsk_bit_array_get_row(&mut_samples, mut_samples_offset, &mut_samples_row);
Expand Down Expand Up @@ -2351,11 +2349,6 @@ compute_general_two_site_stat_result(const tsk_bit_array_t *site_a_state,
tsk_bit_array_t ss_row;
tsk_bit_array_t ss_A_samples, ss_B_samples, ss_AB_samples, AB_samples;

tsk_memset(&ss_A_samples, 0, sizeof(ss_A_samples));
tsk_memset(&ss_B_samples, 0, sizeof(ss_B_samples));
tsk_memset(&ss_AB_samples, 0, sizeof(ss_AB_samples));
tsk_memset(&AB_samples, 0, sizeof(AB_samples));

// Sample sets and b sites are rows, a sites are columns
// b1 b2 b3
// a1 [s1, s2, s3] [s1, s2, s3] [s1, s2, s3]
Expand All @@ -2373,6 +2366,11 @@ compute_general_two_site_stat_result(const tsk_bit_array_t *site_a_state,
double *norm = tsk_malloc(state_dim * sizeof(*norm));
double *result_tmp = tsk_malloc(row_len * num_a_alleles * sizeof(*result_tmp));

tsk_memset(&ss_A_samples, 0, sizeof(ss_A_samples));
tsk_memset(&ss_B_samples, 0, sizeof(ss_B_samples));
tsk_memset(&ss_AB_samples, 0, sizeof(ss_AB_samples));
tsk_memset(&AB_samples, 0, sizeof(AB_samples));

if (weights == NULL || norm == NULL || result_tmp == NULL) {
ret = TSK_ERR_NO_MEMORY;
goto out;
Expand Down Expand Up @@ -2484,15 +2482,15 @@ tsk_treeseq_two_site_count_stat(const tsk_treeseq_t *self, tsk_size_t state_dim,
tsk_size_t site_a, site_b;
bool polarised = false;

tsk_memset(&all_samples_bits, 0, sizeof(all_samples_bits));
tsk_memset(&allele_samples, 0, sizeof(allele_samples));

const tsk_size_t num_sites = self->tables->sites.num_rows;
const tsk_size_t num_samples = self->num_samples;
const tsk_size_t max_alleles = self->tables->mutations.num_rows + num_sites;
tsk_size_t *restrict site_offsets = tsk_malloc(num_sites * sizeof(*site_offsets));
tsk_size_t *restrict num_alleles = tsk_malloc(num_sites * sizeof(*num_alleles));

tsk_memset(&all_samples_bits, 0, sizeof(all_samples_bits));
tsk_memset(&allele_samples, 0, sizeof(allele_samples));

if (site_offsets == NULL || num_alleles == NULL) {
ret = TSK_ERR_NO_MEMORY;
goto out;
Expand Down Expand Up @@ -2620,7 +2618,6 @@ tsk_treeseq_two_locus_count_stat(const tsk_treeseq_t *self, tsk_size_t num_sampl
int ret = 0;

tsk_bit_array_t sample_sets_bits;
tsk_memset(&sample_sets_bits, 0, sizeof(sample_sets_bits));

bool stat_site = !!(options & TSK_STAT_SITE);
bool stat_branch = !!(options & TSK_STAT_BRANCH);
Expand All @@ -2632,6 +2629,8 @@ tsk_treeseq_two_locus_count_stat(const tsk_treeseq_t *self, tsk_size_t num_sampl
.sample_set_sizes = sample_set_sizes,
.set_indexes = set_indexes };

tsk_memset(&sample_sets_bits, 0, sizeof(sample_sets_bits));

ret = tsk_treeseq_check_sample_sets(
self, num_sample_sets, sample_set_sizes, sample_sets);
if (ret != 0) {
Expand Down

0 comments on commit aafb78f

Please sign in to comment.