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Merged
merged 1 commit into from
Nov 4, 2025
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bump to tskit C API 1.2.0 #789

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chore: bump to tskit C API 1.2.0 
BREAKING CHANGE: conversion of table collection
to tree sequence will require mutation parents
to be computed for cases with multiple mutations
at a site.
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@molpopgen
molpopgen committed Nov 4, 2025
commit d768e637fbb74cdd02527a51a8bd1feea37b28ea
36 changes: 22 additions & 14 deletions src/test_fixtures.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -301,10 +301,7 @@ pub mod simulation {

// state variables for site/mutation tables
let num_sites = f64::from(seqlen.into()) as usize;
let mut site_last_mutation_order = vec![0usize; num_sites];

let mut site_last_mutation_tables = vec![MutationId::NULL; num_sites];
let mut site_last_mutation_tr_tbls = vec![MutationId::NULL; num_sites];
let site_last_mutation_order = vec![0usize; num_sites];

let mut site_id_map_tables = vec![SiteId::NULL; num_sites];
let mut site_id_map_tr_tbls = vec![SiteId::NULL; num_sites];
Expand Down Expand Up @@ -387,14 +384,10 @@ pub mod simulation {
tables.add_site(mut_pos as f64, Some(b"a")).unwrap();
}
// add mutation
let parent_mut = site_last_mutation_tables[mut_pos];
let site = site_id_map_tables[mut_pos];
let new_mutation = tables
.add_mutation(site, c, parent_mut, t, Some(derived_state))
let _ = tables
.add_mutation(site, c, MutationId::NULL, t, Some(derived_state))
.unwrap();

site_last_mutation_tables[mut_pos] = new_mutation;
site_last_mutation_order[mut_pos] += 1;
}

find_overlaps(s, e, &intervals, &mut buffer);
Expand All @@ -410,12 +403,10 @@ pub mod simulation {
tr_tbls.add_site(mut_pos as f64, Some(b"a")).unwrap();
}
// add mutation
let parent_mut = site_last_mutation_tr_tbls[mut_pos];
let site = site_id_map_tr_tbls[mut_pos];
let new_mutation = tr_tbls
.add_mutation(site, c, parent_mut, t, Some(derived_state))
let _ = tr_tbls
.add_mutation(site, c, MutationId::NULL, t, Some(derived_state))
.unwrap();
site_last_mutation_tr_tbls[mut_pos] = new_mutation;
}
}
}
Expand Down Expand Up @@ -448,6 +439,23 @@ pub mod simulation {
tables.build_index().unwrap();
tr_tbls.build_index().unwrap();

// Calculate mutation parents
// TODO: need safe API for this.
let code = unsafe {
crate::sys::bindings::tsk_table_collection_compute_mutation_parents(
tables.as_mut_ptr(),
0,
)
};
assert_eq!(code, 0);
let code = unsafe {
crate::sys::bindings::tsk_table_collection_compute_mutation_parents(
tr_tbls.as_mut_ptr(),
0,
)
};
assert_eq!(code, 0);

// to tree sequences
let treeseq_opts = TreeSequenceFlags::default();
let full_trees = TreeSequence::new(tables, treeseq_opts).unwrap();
Expand Down
2 changes: 1 addition & 1 deletion subprojects/tskit/tskit.h
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
/*
* MIT License
*
* Copyright (c) 2019 Tskit Developers
* Copyright (c) 2019-2024 Tskit Developers
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
Expand Down
22 changes: 11 additions & 11 deletions subprojects/tskit/tskit/convert.c
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
/*
* MIT License
*
* Copyright (c) 2018-2021 Tskit Developers
* Copyright (c) 2018-2025 Tskit Developers
* Copyright (c) 2015-2017 University of Oxford
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
Expand Down Expand Up @@ -68,11 +68,11 @@ tsk_newick_converter_run(
const char *label_format = ms_labels ? "%d" : "n%d";

if (root < 0 || root >= (tsk_id_t) self->tree->num_nodes) {
ret = TSK_ERR_NODE_OUT_OF_BOUNDS;
ret = tsk_trace_error(TSK_ERR_NODE_OUT_OF_BOUNDS);
goto out;
}
if (buffer == NULL) {
ret = TSK_ERR_BAD_PARAM_VALUE;
ret = tsk_trace_error(TSK_ERR_BAD_PARAM_VALUE);
goto out;
}
root_parent = tree->parent[root];
Expand All @@ -82,7 +82,7 @@ tsk_newick_converter_run(
v = stack[stack_top];
if (tree->left_child[v] != TSK_NULL && v != u) {
if (s >= buffer_size) {
ret = TSK_ERR_BUFFER_OVERFLOW;
ret = tsk_trace_error(TSK_ERR_BUFFER_OVERFLOW);
goto out;
}
buffer[s] = '(';
Expand All @@ -104,17 +104,17 @@ tsk_newick_converter_run(
}
if (label != -1) {
if (s >= buffer_size) {
ret = TSK_ERR_BUFFER_OVERFLOW;
ret = tsk_trace_error(TSK_ERR_BUFFER_OVERFLOW);
goto out;
}
r = snprintf(buffer + s, buffer_size - s, label_format, label);
if (r < 0) {
ret = TSK_ERR_IO;
ret = tsk_trace_error(TSK_ERR_IO);
goto out;
}
s += (size_t) r;
if (s >= buffer_size) {
ret = TSK_ERR_BUFFER_OVERFLOW;
ret = tsk_trace_error(TSK_ERR_BUFFER_OVERFLOW);
goto out;
}
}
Expand All @@ -123,12 +123,12 @@ tsk_newick_converter_run(
r = snprintf(buffer + s, buffer_size - s, ":%.*f", (int) self->precision,
branch_length);
if (r < 0) {
ret = TSK_ERR_IO;
ret = tsk_trace_error(TSK_ERR_IO);
goto out;
}
s += (size_t) r;
if (s >= buffer_size) {
ret = TSK_ERR_BUFFER_OVERFLOW;
ret = tsk_trace_error(TSK_ERR_BUFFER_OVERFLOW);
goto out;
}
if (v == tree->right_child[u]) {
Expand All @@ -141,7 +141,7 @@ tsk_newick_converter_run(
}
}
if ((s + 1) >= buffer_size) {
ret = TSK_ERR_BUFFER_OVERFLOW;
ret = tsk_trace_error(TSK_ERR_BUFFER_OVERFLOW);
goto out;
}
buffer[s] = ';';
Expand All @@ -164,7 +164,7 @@ tsk_newick_converter_init(tsk_newick_converter_t *self, const tsk_tree_t *tree,
self->traversal_stack
= tsk_malloc(tsk_tree_get_size_bound(tree) * sizeof(*self->traversal_stack));
if (self->traversal_stack == NULL) {
ret = TSK_ERR_NO_MEMORY;
ret = tsk_trace_error(TSK_ERR_NO_MEMORY);
goto out;
}
out:
Expand Down
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