Change genotypes to 32bit

Author: benjeffery

c/CHANGELOG.rst

@@ -2,7 +2,14 @@
 [0.99.16] - 2022-0X-XX
 ----------------------
 
-- Make dumping of tables and tree seqences to disk a zero-copy operation.
+**Breaking changes**
+
+- Change the type of genotypes to ``int32_t``, removing the TSK_16_BIT_GENOTYPES flag option.
+  (:user:`benjeffery`, :issue:`463`, :pr:`2108`)
+
+**Features**
+
+- Make dumping of tables and tree sequences to disk a zero-copy operation.
   (:user:`benjeffery`, :issue:`2111`, :pr:`2124`)
 
 ----------------------

c/tests/test_genotypes.c

@@ -49,7 +49,7 @@ tsk_ls_hmm_next_probability_test(tsk_ls_hmm_t *TSK_UNUSED(self),
 }
 
 static int
-run_test_hmm(tsk_ls_hmm_t *hmm, int8_t *haplotype, tsk_compressed_matrix_t *output)
+run_test_hmm(tsk_ls_hmm_t *hmm, int32_t *haplotype, tsk_compressed_matrix_t *output)
 {
     int ret = 0;
 
@@ -79,7 +79,7 @@ test_single_tree_missing_alleles(void)
 
     double rho[] = { 0, 0.25, 0.25 };
     double mu[] = { 0.125, 0.125, 0.125 };
-    int8_t h[] = { 0, 0, 0, 0 };
+    int32_t h[] = { 0, 0, 0, 0 };
 
     tsk_treeseq_from_text(&ts, 1, single_tree_ex_nodes, single_tree_ex_edges, NULL,
         single_tree_ex_sites, single_tree_ex_mutations, NULL, NULL, 0);
@@ -108,7 +108,7 @@ test_single_tree_exact_match(void)
 
     double rho[] = { 0.0, 0.25, 0.25 };
     double mu[] = { 0, 0, 0 };
-    int8_t h[] = { 1, 1, 1 };
+    int32_t h[] = { 1, 1, 1 };
     tsk_id_t path[3];
     double decoded_compressed_matrix[12];
     unsigned int precision;
@@ -167,7 +167,7 @@ test_single_tree_missing_haplotype_data(void)
 
     double rho[] = { 0.0, 0.25, 0.25 };
     double mu[] = { 0, 0, 0 };
-    int8_t h[] = { 1, TSK_MISSING_DATA, 1 };
+    int32_t h[] = { 1, TSK_MISSING_DATA, 1 };
     tsk_id_t path[3];
     double decoded_compressed_matrix[12];
 
@@ -211,7 +211,7 @@ test_single_tree_match_impossible(void)
     double rho[] = { 0.0, 0.25, 0.25 };
     double mu[] = { 0, 0, 0 };
     /* This haplotype can't happen with a mutation rate of 0 */
-    int8_t h[] = { 0, 0, 0 };
+    int32_t h[] = { 0, 0, 0 };
 
     tsk_treeseq_from_text(&ts, 1, single_tree_ex_nodes, single_tree_ex_edges, NULL,
         single_tree_ex_sites, single_tree_ex_mutations, NULL, NULL, 0);
@@ -247,7 +247,7 @@ test_single_tree_errors(void)
 
     double rho[] = { 0.0, 0.25, 0.25 };
     double mu[] = { 0, 0, 0 };
-    int8_t h[] = { 0, 0, 0 };
+    int32_t h[] = { 0, 0, 0 };
 
     tsk_treeseq_from_text(&ts, 1, single_tree_ex_nodes, single_tree_ex_edges, NULL,
         single_tree_ex_sites, single_tree_ex_mutations, NULL, NULL, 0);
@@ -309,7 +309,7 @@ test_single_tree_compressed_matrix(void)
 
     double rho[] = { 0.0, 0.25, 0.25 };
     double mu[] = { 0.1, 0.1, 0.1 };
-    int8_t h[] = { 0, 0, 0 };
+    int32_t h[] = { 0, 0, 0 };
 
     tsk_treeseq_from_text(&ts, 1, single_tree_ex_nodes, single_tree_ex_edges, NULL,
         single_tree_ex_sites, single_tree_ex_mutations, NULL, NULL, 0);
@@ -374,7 +374,7 @@ test_single_tree_viterbi_matrix(void)
     tsk_ls_hmm_t ls_hmm;
     double rho[] = { 0.0, 0.25, 0.25 };
     double mu[] = { 0, 0, 0 };
-    int8_t h[] = { 1, 1, 1 };
+    int32_t h[] = { 1, 1, 1 };
     tsk_id_t path[3];
     tsk_value_transition_t T[2];
     int j;
@@ -448,7 +448,7 @@ test_multi_tree_exact_match(void)
 
     double rho[] = { 0.0, 0.25, 0.25 };
     double mu[] = { 0, 0, 0 };
-    int8_t h[] = { 1, 1, 1 };
+    int32_t h[] = { 1, 1, 1 };
     tsk_id_t path[3];
     double decoded_compressed_matrix[12];
     unsigned int precision;
@@ -530,7 +530,7 @@ test_caterpillar_tree_many_values(void)
     tsk_ls_hmm_t ls_hmm;
     tsk_compressed_matrix_t matrix;
     double unused[] = { 0, 0, 0, 0, 0 };
-    int8_t h[] = { 0, 0, 0, 0, 0 };
+    int32_t h[] = { 0, 0, 0, 0, 0 };
     tsk_size_t n[] = {
         8,
         16,

c/tests/test_haplotype_matching.c

@@ -486,7 +486,7 @@ verify_simplify_genotypes(tsk_treeseq_t *ts, tsk_treeseq_t *subset,
     tsk_vargen_t vargen, subset_vargen;
     tsk_variant_t *variant, *subset_variant;
     tsk_size_t j, k;
-    int8_t a1, a2;
+    int32_t a1, a2;
     const tsk_id_t *sample_index_map;
 
     sample_index_map = tsk_treeseq_get_sample_index_map(ts);
@@ -511,8 +511,8 @@ verify_simplify_genotypes(tsk_treeseq_t *ts, tsk_treeseq_t *subset,
         CU_ASSERT_EQUAL(variant->site->position, subset_variant->site->position);
         for (k = 0; k < num_samples; k++) {
             CU_ASSERT_FATAL(sample_index_map[samples[k]] < (tsk_id_t) ts->num_samples);
-            a1 = variant->genotypes.i8[sample_index_map[samples[k]]];
-            a2 = subset_variant->genotypes.i8[k];
+            a1 = variant->genotypes[sample_index_map[samples[k]]];
+            a2 = subset_variant->genotypes[k];
             /* printf("a1 = %d, a2 = %d\n", a1, a2); */
             /* printf("k = %d original node = %d " */
             /*         "original_index = %d a1=%.*s a2=%.*s\n", */
@@ -1330,29 +1330,29 @@ test_simplest_non_sample_leaf_records(void)
     CU_ASSERT_EQUAL_FATAL(ret, 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->genotypes.i8[0], 1);
-    CU_ASSERT_EQUAL(var->genotypes.i8[1], 0);
+    CU_ASSERT_EQUAL(var->genotypes[0], 1);
+    CU_ASSERT_EQUAL(var->genotypes[1], 0);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->genotypes.i8[0], 0);
-    CU_ASSERT_EQUAL(var->genotypes.i8[1], 1);
+    CU_ASSERT_EQUAL(var->genotypes[0], 0);
+    CU_ASSERT_EQUAL(var->genotypes[1], 1);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->genotypes.i8[0], 0);
-    CU_ASSERT_EQUAL(var->genotypes.i8[1], 0);
+    CU_ASSERT_EQUAL(var->genotypes[0], 0);
+    CU_ASSERT_EQUAL(var->genotypes[1], 0);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->genotypes.i8[0], 0);
-    CU_ASSERT_EQUAL(var->genotypes.i8[1], 0);
+    CU_ASSERT_EQUAL(var->genotypes[0], 0);
+    CU_ASSERT_EQUAL(var->genotypes[1], 0);
 
     ret = tsk_vargen_next(&vargen, &var);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
@@ -1659,9 +1659,9 @@ test_simplest_back_mutations(void)
     CU_ASSERT_EQUAL(var->num_alleles, 2);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[0], "0", 1);
     CU_ASSERT_NSTRING_EQUAL(var->alleles[1], "1", 1);
-    CU_ASSERT_EQUAL(var->genotypes.i8[0], 0);
-    CU_ASSERT_EQUAL(var->genotypes.i8[1], 1);
-    CU_ASSERT_EQUAL(var->genotypes.i8[2], 0);
+    CU_ASSERT_EQUAL(var->genotypes[0], 0);
+    CU_ASSERT_EQUAL(var->genotypes[1], 1);
+    CU_ASSERT_EQUAL(var->genotypes[2], 0);
     CU_ASSERT_EQUAL(var->site->id, 0);
     CU_ASSERT_EQUAL(var->site->mutations_length, 2);
     tsk_vargen_free(&vargen);
@@ -3069,10 +3069,10 @@ test_simplest_map_mutations(void)
     const char *edges = "0  1   2   0,1\n";
     tsk_treeseq_t ts;
     tsk_tree_t t;
-    int8_t genotypes[] = { 0, 0 };
+    int32_t genotypes[] = { 0, 0 };
     tsk_size_t num_transitions;
     tsk_state_transition_t *transitions;
-    int8_t ancestral_state;
+    int32_t ancestral_state;
     int ret;
 
     tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, NULL, NULL, NULL, NULL, 0);
@@ -3151,10 +3151,10 @@ test_simplest_nonbinary_map_mutations(void)
     const char *edges = "0  1   4   0,1,2,3\n";
     tsk_treeseq_t ts;
     tsk_tree_t t;
-    int8_t genotypes[] = { 0, 0, 0, 0 };
+    int32_t genotypes[] = { 0, 0, 0, 0 };
     tsk_size_t num_transitions;
     tsk_state_transition_t *transitions;
-    int8_t ancestral_state;
+    int32_t ancestral_state;
     int ret;
 
     tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, NULL, NULL, NULL, NULL, 0);
@@ -3197,10 +3197,10 @@ test_simplest_unary_map_mutations(void)
                         "0  1   4   2,3\n";
     tsk_treeseq_t ts;
     tsk_tree_t t;
-    int8_t genotypes[] = { 0, 0 };
+    int32_t genotypes[] = { 0, 0 };
     tsk_size_t num_transitions;
     tsk_state_transition_t *transitions;
-    int8_t ancestral_state;
+    int32_t ancestral_state;
     int ret;
 
     tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, NULL, NULL, NULL, NULL, 0);
@@ -3241,10 +3241,10 @@ test_simplest_non_sample_leaf_map_mutations(void)
     const char *edges = "0  1   2   0,1,3,4\n";
     tsk_treeseq_t ts;
     tsk_tree_t t;
-    int8_t genotypes[] = { 0, 0 };
+    int32_t genotypes[] = { 0, 0 };
     tsk_size_t num_transitions;
     tsk_state_transition_t *transitions;
-    int8_t ancestral_state;
+    int32_t ancestral_state;
     int ret;
 
     tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, NULL, NULL, NULL, NULL, 0);
@@ -3283,10 +3283,10 @@ test_simplest_internal_sample_map_mutations(void)
     const char *edges = "0  1   2   0,1\n";
     tsk_treeseq_t ts;
     tsk_tree_t t;
-    int8_t genotypes[] = { 0, 0, 0 };
+    int32_t genotypes[] = { 0, 0, 0 };
     tsk_size_t num_transitions;
     tsk_state_transition_t *transitions;
-    int8_t ancestral_state;
+    int32_t ancestral_state;
     int ret;
 
     tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, NULL, NULL, NULL, NULL, 0);
@@ -3340,10 +3340,10 @@ test_simplest_multiple_root_map_mutations(void)
                         "0  1   5   2,3\n";
     tsk_treeseq_t ts;
     tsk_tree_t t;
-    int8_t genotypes[] = { 0, 0, 0, 0 };
+    int32_t genotypes[] = { 0, 0, 0, 0 };
     tsk_size_t num_transitions;
     tsk_state_transition_t *transitions;
-    int8_t ancestral_state;
+    int32_t ancestral_state;
     int ret;
 
     tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, NULL, NULL, NULL, NULL, 0);
@@ -3397,10 +3397,10 @@ test_simplest_chained_map_mutations(void)
                         "0  1   4   2,3\n";
     tsk_treeseq_t ts;
     tsk_tree_t t;
-    int8_t genotypes[] = { 0, 0, 0, 0 };
+    int32_t genotypes[] = { 0, 0, 0, 0 };
     tsk_size_t num_transitions;
     tsk_state_transition_t *transitions;
-    int8_t ancestral_state;
+    int32_t ancestral_state;
     int ret;
 
     tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, NULL, NULL, NULL, NULL, 0);
@@ -4543,11 +4543,11 @@ test_single_tree_map_mutations(void)
 {
     tsk_treeseq_t ts;
     tsk_tree_t t;
-    int8_t genotypes[] = { 0, 1, 1, 1 };
+    int32_t genotypes[] = { 0, 1, 1, 1 };
     int ret = 0;
     tsk_size_t num_transitions;
     tsk_state_transition_t *transitions;
-    int8_t ancestral_state, j;
+    int32_t ancestral_state, j;
 
     tsk_treeseq_from_text(&ts, 1, single_tree_ex_nodes, single_tree_ex_edges, NULL, NULL,
         NULL, NULL, NULL, 0);
@@ -4689,11 +4689,11 @@ test_single_tree_map_mutations_internal_samples(void)
                         "0.00000000      1.00000000      8       7\n";
     tsk_treeseq_t ts;
     tsk_tree_t t;
-    int8_t genotypes[] = { 0, 2, 2, 1, 0 };
+    int32_t genotypes[] = { 0, 2, 2, 1, 0 };
     int ret = 0;
     tsk_size_t num_transitions;
     tsk_state_transition_t *transitions;
-    int8_t ancestral_state;
+    int32_t ancestral_state;
 
     tsk_treeseq_from_text(&ts, 1, nodes, edges, NULL, NULL, NULL, NULL, NULL, 0);
     CU_ASSERT_EQUAL(tsk_treeseq_get_num_samples(&ts), 5);