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Merge pull request #778 from jeromekelleher/mutations-over-samples-not-missing
Fix bugs in missing data handling.
2 parents c5c639f + 5b4a541 commit 436b1ea

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5 files changed

+394
-25
lines changed

5 files changed

+394
-25
lines changed

‎c/CHANGELOG.rst‎

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Original file line numberDiff line numberDiff line change
@@ -12,6 +12,14 @@
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from the MRCAs of samples in the simplified tree sequence back to the roots
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in the input tree sequence (:user:`jeromekelleher`, :issue:`775`, :pr:`782`).
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**Bugfixes**
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- :issue:`777` - Mutations over isolated samples were incorrectly decoded as
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missing data. (:user:`jeromekelleher`, :pr:`778`)
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- :issue:`776` - Fix a segfault when a partial list of samples
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was provided to the ``variants`` iterator. (:user:`jeromekelleher`, :pr:`778`)
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---------------------
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[0.99.4] - 2020-08-12
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---------------------

‎c/tests/test_genotypes.c‎

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Original file line numberDiff line numberDiff line change
@@ -93,6 +93,7 @@ test_simplest_missing_data_user_alleles(void)
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tsk_variant_t *var;
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const char *alleles[] = { "A", NULL };
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int ret;
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tsk_id_t samples[] = { 0 };
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tsk_treeseq_from_text(&ts, 1, nodes, "", NULL, sites, NULL, NULL, NULL, 0);
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CU_ASSERT_EQUAL(tsk_treeseq_get_num_samples(&ts), 2);
@@ -110,6 +111,17 @@ test_simplest_missing_data_user_alleles(void)
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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tsk_vargen_free(&vargen);
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ret = tsk_vargen_init(&vargen, &ts, samples, 1, alleles, 0);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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ret = tsk_vargen_next(&vargen, &var);
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CU_ASSERT_EQUAL_FATAL(ret, 1);
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CU_ASSERT_EQUAL(var->site->position, 0.0);
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CU_ASSERT_TRUE(var->has_missing_data);
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CU_ASSERT_EQUAL(var->genotypes.i8[0], TSK_MISSING_DATA);
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ret = tsk_vargen_next(&vargen, &var);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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tsk_vargen_free(&vargen);
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ret = tsk_vargen_init(&vargen, &ts, NULL, 0, NULL, TSK_16_BIT_GENOTYPES);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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ret = tsk_vargen_next(&vargen, &var);
@@ -122,6 +134,17 @@ test_simplest_missing_data_user_alleles(void)
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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tsk_vargen_free(&vargen);
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ret = tsk_vargen_init(&vargen, &ts, samples, 1, alleles, TSK_16_BIT_GENOTYPES);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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ret = tsk_vargen_next(&vargen, &var);
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CU_ASSERT_EQUAL_FATAL(ret, 1);
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CU_ASSERT_EQUAL(var->site->position, 0.0);
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CU_ASSERT_TRUE(var->has_missing_data);
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CU_ASSERT_EQUAL(var->genotypes.i8[0], TSK_MISSING_DATA);
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ret = tsk_vargen_next(&vargen, &var);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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tsk_vargen_free(&vargen);
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ret = tsk_vargen_init(&vargen, &ts, NULL, 0, NULL, TSK_ISOLATED_NOT_MISSING);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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ret = tsk_vargen_next(&vargen, &var);
@@ -137,6 +160,161 @@ test_simplest_missing_data_user_alleles(void)
137160
tsk_treeseq_free(&ts);
138161
}
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static void
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test_simplest_missing_data_mutations(void)
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{
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const char *nodes = "1 0 0\n"
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"1 0 0\n";
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const char *sites = "0.0 A\n";
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const char *mutations = "0 0 T -1\n";
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tsk_treeseq_t ts;
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tsk_vargen_t vargen;
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tsk_variant_t *var;
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const char *alleles[] = { "A", "T", NULL };
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int ret;
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tsk_id_t samples[] = { 0 };
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tsk_treeseq_from_text(&ts, 1, nodes, "", NULL, sites, mutations, NULL, NULL, 0);
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CU_ASSERT_EQUAL(tsk_treeseq_get_num_samples(&ts), 2);
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CU_ASSERT_EQUAL(tsk_treeseq_get_num_sites(&ts), 1);
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CU_ASSERT_EQUAL(tsk_treeseq_get_num_mutations(&ts), 1);
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ret = tsk_vargen_init(&vargen, &ts, NULL, 0, alleles, 0);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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ret = tsk_vargen_next(&vargen, &var);
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CU_ASSERT_EQUAL_FATAL(ret, 1);
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CU_ASSERT_EQUAL(var->site->position, 0.0);
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CU_ASSERT_TRUE(var->has_missing_data);
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CU_ASSERT_EQUAL(var->genotypes.i8[0], 1);
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CU_ASSERT_EQUAL(var->genotypes.i8[1], TSK_MISSING_DATA);
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ret = tsk_vargen_next(&vargen, &var);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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tsk_vargen_free(&vargen);
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ret = tsk_vargen_init(&vargen, &ts, NULL, 0, alleles, TSK_16_BIT_GENOTYPES);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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ret = tsk_vargen_next(&vargen, &var);
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CU_ASSERT_EQUAL_FATAL(ret, 1);
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CU_ASSERT_EQUAL(var->site->position, 0.0);
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CU_ASSERT_TRUE(var->has_missing_data);
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CU_ASSERT_EQUAL(var->genotypes.i16[0], 1);
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CU_ASSERT_EQUAL(var->genotypes.i16[1], TSK_MISSING_DATA);
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ret = tsk_vargen_next(&vargen, &var);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
204+
tsk_vargen_free(&vargen);
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206+
ret = tsk_vargen_init(&vargen, &ts, samples, 1, alleles, 0);
207+
CU_ASSERT_EQUAL_FATAL(ret, 0);
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tsk_vargen_print_state(&vargen, _devnull);
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ret = tsk_vargen_next(&vargen, &var);
210+
CU_ASSERT_EQUAL_FATAL(ret, 1);
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CU_ASSERT_EQUAL(var->site->position, 0.0);
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CU_ASSERT_FALSE(var->has_missing_data);
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CU_ASSERT_EQUAL(var->genotypes.i8[0], 1);
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ret = tsk_vargen_next(&vargen, &var);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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tsk_vargen_free(&vargen);
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ret = tsk_vargen_init(&vargen, &ts, samples, 1, alleles, TSK_16_BIT_GENOTYPES);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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tsk_vargen_print_state(&vargen, _devnull);
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ret = tsk_vargen_next(&vargen, &var);
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CU_ASSERT_EQUAL_FATAL(ret, 1);
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CU_ASSERT_EQUAL(var->site->position, 0.0);
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CU_ASSERT_FALSE(var->has_missing_data);
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CU_ASSERT_EQUAL(var->genotypes.i16[0], 1);
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ret = tsk_vargen_next(&vargen, &var);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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tsk_vargen_free(&vargen);
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230+
ret = tsk_vargen_init(&vargen, &ts, NULL, 0, NULL, TSK_ISOLATED_NOT_MISSING);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
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ret = tsk_vargen_next(&vargen, &var);
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CU_ASSERT_EQUAL_FATAL(ret, 1);
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CU_ASSERT_EQUAL(var->site->position, 0.0);
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CU_ASSERT_FALSE(var->has_missing_data);
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CU_ASSERT_EQUAL(var->genotypes.i8[0], 1);
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CU_ASSERT_EQUAL(var->genotypes.i8[1], 0);
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ret = tsk_vargen_next(&vargen, &var);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
240+
tsk_vargen_free(&vargen);
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242+
tsk_treeseq_free(&ts);
243+
}
244+
245+
static void
246+
test_simplest_missing_data_mutations_all_samples(void)
247+
{
248+
const char *nodes = "1 0 0\n"
249+
"1 0 0\n";
250+
const char *sites = "0.0 A\n";
251+
const char *mutations = "0 0 T -1\n"
252+
"0 1 T -1\n";
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tsk_treeseq_t ts;
254+
tsk_vargen_t vargen;
255+
tsk_variant_t *var;
256+
const char *alleles[] = { "A", "T", NULL };
257+
int ret;
258+
tsk_id_t samples[] = { 0, 1 };
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260+
tsk_treeseq_from_text(&ts, 1, nodes, "", NULL, sites, mutations, NULL, NULL, 0);
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CU_ASSERT_EQUAL(tsk_treeseq_get_num_samples(&ts), 2);
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CU_ASSERT_EQUAL(tsk_treeseq_get_num_sites(&ts), 1);
263+
CU_ASSERT_EQUAL(tsk_treeseq_get_num_mutations(&ts), 2);
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265+
ret = tsk_vargen_init(&vargen, &ts, NULL, 0, alleles, 0);
266+
CU_ASSERT_EQUAL_FATAL(ret, 0);
267+
ret = tsk_vargen_next(&vargen, &var);
268+
CU_ASSERT_EQUAL_FATAL(ret, 1);
269+
CU_ASSERT_EQUAL(var->site->position, 0.0);
270+
CU_ASSERT_FALSE(var->has_missing_data);
271+
CU_ASSERT_EQUAL(var->genotypes.i8[0], 1);
272+
CU_ASSERT_EQUAL(var->genotypes.i8[1], 1);
273+
ret = tsk_vargen_next(&vargen, &var);
274+
CU_ASSERT_EQUAL_FATAL(ret, 0);
275+
tsk_vargen_free(&vargen);
276+
277+
ret = tsk_vargen_init(&vargen, &ts, samples, 2, alleles, 0);
278+
CU_ASSERT_EQUAL_FATAL(ret, 0);
279+
tsk_vargen_print_state(&vargen, _devnull);
280+
ret = tsk_vargen_next(&vargen, &var);
281+
CU_ASSERT_EQUAL_FATAL(ret, 1);
282+
CU_ASSERT_EQUAL(var->site->position, 0.0);
283+
CU_ASSERT_FALSE(var->has_missing_data);
284+
CU_ASSERT_EQUAL(var->genotypes.i8[0], 1);
285+
CU_ASSERT_EQUAL(var->genotypes.i8[1], 1);
286+
ret = tsk_vargen_next(&vargen, &var);
287+
CU_ASSERT_EQUAL_FATAL(ret, 0);
288+
tsk_vargen_free(&vargen);
289+
290+
ret = tsk_vargen_init(&vargen, &ts, samples, 2, alleles, TSK_16_BIT_GENOTYPES);
291+
CU_ASSERT_EQUAL_FATAL(ret, 0);
292+
tsk_vargen_print_state(&vargen, _devnull);
293+
ret = tsk_vargen_next(&vargen, &var);
294+
CU_ASSERT_EQUAL_FATAL(ret, 1);
295+
CU_ASSERT_EQUAL(var->site->position, 0.0);
296+
CU_ASSERT_FALSE(var->has_missing_data);
297+
CU_ASSERT_EQUAL(var->genotypes.i16[0], 1);
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CU_ASSERT_EQUAL(var->genotypes.i16[1], 1);
299+
ret = tsk_vargen_next(&vargen, &var);
300+
CU_ASSERT_EQUAL_FATAL(ret, 0);
301+
tsk_vargen_free(&vargen);
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303+
ret = tsk_vargen_init(&vargen, &ts, NULL, 0, NULL, TSK_ISOLATED_NOT_MISSING);
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CU_ASSERT_EQUAL_FATAL(ret, 0);
305+
ret = tsk_vargen_next(&vargen, &var);
306+
CU_ASSERT_EQUAL_FATAL(ret, 1);
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CU_ASSERT_EQUAL(var->site->position, 0.0);
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CU_ASSERT_FALSE(var->has_missing_data);
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CU_ASSERT_EQUAL(var->genotypes.i8[0], 1);
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CU_ASSERT_EQUAL(var->genotypes.i8[1], 1);
311+
ret = tsk_vargen_next(&vargen, &var);
312+
CU_ASSERT_EQUAL_FATAL(ret, 0);
313+
tsk_vargen_free(&vargen);
314+
315+
tsk_treeseq_free(&ts);
316+
}
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140318
static void
141319
test_single_tree_user_alleles(void)
142320
{
@@ -733,6 +911,9 @@ main(int argc, char **argv)
733911
{ "test_simplest_missing_data", test_simplest_missing_data },
734912
{ "test_simplest_missing_data_user_alleles",
735913
test_simplest_missing_data_user_alleles },
914+
{ "test_simplest_missing_data_mutations", test_simplest_missing_data_mutations },
915+
{ "test_simplest_missing_data_mutations_all_samples",
916+
test_simplest_missing_data_mutations_all_samples },
736917
{ "test_single_tree_user_alleles", test_single_tree_user_alleles },
737918
{ "test_single_tree_char_alphabet", test_single_tree_char_alphabet },
738919
{ "test_single_tree_binary_alphabet", test_single_tree_binary_alphabet },

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