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Change diff iter types to tsk_ equivalents #788

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Change diff iter types to tsk_ equivalents #788

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2 changes: 1 addition & 1 deletion c/tests/test_trees.c
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Original file line number Diff line number Diff line change
Expand Up @@ -175,7 +175,7 @@ verify_individual_nodes(tsk_treeseq_t *ts)
}

static void
verify_trees(tsk_treeseq_t *ts, uint32_t num_trees, tsk_id_t *parents)
verify_trees(tsk_treeseq_t *ts, tsk_size_t num_trees, tsk_id_t *parents)
{
int ret;
tsk_id_t u, j, v;
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16 changes: 8 additions & 8 deletions c/tskit/trees.c
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Original file line number Diff line number Diff line change
Expand Up @@ -4383,7 +4383,7 @@ tsk_diff_iter_init(tsk_diff_iter_t *self, tsk_treeseq_t *tree_sequence)
self->insertion_index = 0;
self->removal_index = 0;
self->tree_left = 0;
self->tree_index = (size_t) -1;
self->tree_index = -1;
self->edge_list_nodes = malloc(self->num_edges * sizeof(*self->edge_list_nodes));
if (self->edge_list_nodes == NULL) {
ret = TSK_ERR_NO_MEMORY;
Expand Down Expand Up @@ -4420,7 +4420,7 @@ tsk_diff_iter_next(tsk_diff_iter_t *self, double *ret_left, double *ret_right,
const double sequence_length = self->tree_sequence->tables->sequence_length;
double left = self->tree_left;
double right = sequence_length;
size_t next_edge_list_node = 0;
tsk_size_t next_edge_list_node = 0;
tsk_treeseq_t *s = self->tree_sequence;
tsk_edge_list_node_t *out_head = NULL;
tsk_edge_list_node_t *out_tail = NULL;
Expand All @@ -4429,17 +4429,17 @@ tsk_diff_iter_next(tsk_diff_iter_t *self, double *ret_left, double *ret_right,
tsk_edge_list_node_t *w = NULL;
tsk_edge_list_t edges_out;
tsk_edge_list_t edges_in;
size_t num_trees = tsk_treeseq_get_num_trees(s);
tsk_size_t num_trees = tsk_treeseq_get_num_trees(s);
const tsk_edge_table_t *edges = &s->tables->edges;
const tsk_id_t *insertion_order = s->tables->indexes.edge_insertion_order;
const tsk_id_t *removal_order = s->tables->indexes.edge_removal_order;

memset(&edges_out, 0, sizeof(edges_out));
memset(&edges_in, 0, sizeof(edges_in));

if (self->tree_index + 1 < num_trees) {
if (self->tree_index + 1 < (tsk_id_t) num_trees) {
/* First we remove the stale records */
while (self->removal_index < self->num_edges
while (self->removal_index < (tsk_id_t) self->num_edges
&& left == edges->right[removal_order[self->removal_index]]) {
k = removal_order[self->removal_index];
assert(next_edge_list_node < self->num_edges);
Expand Down Expand Up @@ -4469,7 +4469,7 @@ tsk_diff_iter_next(tsk_diff_iter_t *self, double *ret_left, double *ret_right,
edges_out.tail = out_tail;

/* Now insert the new records */
while (self->insertion_index < self->num_edges
while (self->insertion_index < (tsk_id_t) self->num_edges
&& left == edges->left[insertion_order[self->insertion_index]]) {
k = insertion_order[self->insertion_index];
assert(next_edge_list_node < self->num_edges);
Expand Down Expand Up @@ -4499,10 +4499,10 @@ tsk_diff_iter_next(tsk_diff_iter_t *self, double *ret_left, double *ret_right,
edges_in.tail = in_tail;

right = sequence_length;
if (self->insertion_index < self->num_edges) {
if (self->insertion_index < (tsk_id_t) self->num_edges) {
right = TSK_MIN(right, edges->left[insertion_order[self->insertion_index]]);
}
if (self->removal_index < self->num_edges) {
if (self->removal_index < (tsk_id_t) self->num_edges) {
right = TSK_MIN(right, edges->right[removal_order[self->removal_index]]);
}
self->tree_index++;
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10 changes: 5 additions & 5 deletions c/tskit/trees.h
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Expand Up @@ -198,13 +198,13 @@ typedef struct {
} tsk_edge_list_t;

typedef struct {
size_t num_nodes;
size_t num_edges;
tsk_size_t num_nodes;
tsk_size_t num_edges;
double tree_left;
tsk_treeseq_t *tree_sequence;
size_t insertion_index;
size_t removal_index;
size_t tree_index;
tsk_id_t insertion_index;
tsk_id_t removal_index;
tsk_id_t tree_index;
tsk_edge_list_node_t *edge_list_nodes;
} tsk_diff_iter_t;

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2 changes: 1 addition & 1 deletion python/_tskitmodule.c
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Original file line number Diff line number Diff line change
Expand Up @@ -9888,7 +9888,7 @@ TreeDiffIterator_next(TreeDiffIterator *self)
PyObject *value = NULL;
int err;
double left, right;
size_t list_size, j;
tsk_size_t list_size, j;
tsk_edge_list_node_t *record;
tsk_edge_list_t records_out, records_in;

Expand Down