C lib changes for precision->likelihood_threshold

Author: jeromekelleher

Diff for: lib/ancestor_matcher.c

@@ -103,7 +103,7 @@ ancestor_matcher_print_state(ancestor_matcher_t *self, FILE *out)
 int
 ancestor_matcher_alloc(ancestor_matcher_t *self,
     tree_sequence_builder_t *tree_sequence_builder, double *recombination_rate,
-    double *mismatch_rate, unsigned int precision, int flags)
+    double *mismatch_rate, double likelihood_threshold, int flags)
 {
     int ret = 0;
     /* TODO make these input parameters. */
@@ -112,7 +112,7 @@ ancestor_matcher_alloc(ancestor_matcher_t *self,
     memset(self, 0, sizeof(ancestor_matcher_t));
     /* All allocs for arrays related to nodes are done in expand_nodes */
     self->flags = flags;
-    self->precision = precision;
+    self->likelihood_threshold = likelihood_threshold;
     self->max_nodes = 0;
     self->tree_sequence_builder = tree_sequence_builder;
     self->num_sites = tree_sequence_builder->num_sites;
@@ -366,7 +366,7 @@ ancestor_matcher_update_site_likelihood_values(ancestor_matcher_t *self,
     /* Renormalise the likelihoods. */
     for (j = 0; j < num_likelihood_nodes; j++) {
         u = L_nodes[j];
-        L[u] = tsk_round(L[u] / max_L, self->precision);
+        L[u] = TSK_MAX(L[u] / max_L, self->likelihood_threshold);
     }
     ancestor_matcher_unset_allelic_state(self, site, allelic_state);
 out:

Diff for: lib/tests/tests.c

@@ -364,7 +364,7 @@ run_random_data(size_t num_samples, size_t num_sites, int seed,
     ret = tree_sequence_builder_alloc(&tsb, num_sites, NULL, 1, 1, 0);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = ancestor_matcher_alloc(&ancestor_matcher, &tsb, recombination_rates,
-        mismatch_rates, 6, TSI_EXTENDED_CHECKS);
+        mismatch_rates, DBL_MIN, TSI_EXTENDED_CHECKS);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
 
     for (j = 0; j < num_sites; j++) {
@@ -536,7 +536,7 @@ test_matching_one_site(void)
     CU_ASSERT_EQUAL_FATAL(ret, 0);
 
     ret = ancestor_matcher_alloc(
-        &ancestor_matcher, &tsb, &recombination_rate, &mismatch_rate, 12, 0);
+        &ancestor_matcher, &tsb, &recombination_rate, &mismatch_rate, DBL_MIN, 0);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
 
     ret = ancestor_matcher_find_path(
@@ -623,7 +623,7 @@ test_matching_one_site_many_alleles(void)
     CU_ASSERT_EQUAL_FATAL(ret, 0);
 
     ret = ancestor_matcher_alloc(
-        &ancestor_matcher, &tsb, &recombination_rate, &mismatch_rate, 12, 0);
+        &ancestor_matcher, &tsb, &recombination_rate, &mismatch_rate, DBL_MIN, 0);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
 
     haplotype = 0;
@@ -682,7 +682,7 @@ test_matching_errors(void)
     CU_ASSERT_EQUAL_FATAL(ret, 0);
 
     ret = ancestor_matcher_alloc(
-        &ancestor_matcher, &tsb, recombination_rate, mismatch_rate, 12, 0);
+        &ancestor_matcher, &tsb, recombination_rate, mismatch_rate, DBL_MIN, 0);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = ancestor_matcher_find_path(
         &ancestor_matcher, 0, 2, haplotype, match, &num_edges, &left, &right, &parent);
@@ -692,7 +692,7 @@ test_matching_errors(void)
     haplotype[0] = 0;
     mismatch_rate[0] = 1;
     ret = ancestor_matcher_alloc(
-        &ancestor_matcher, &tsb, recombination_rate, mismatch_rate, 12, 0);
+        &ancestor_matcher, &tsb, recombination_rate, mismatch_rate, DBL_MIN, 0);
     CU_ASSERT_EQUAL_FATAL(ret, 0);
     ret = ancestor_matcher_find_path(
         &ancestor_matcher, 0, 2, haplotype, match, &num_edges, &left, &right, &parent);

Diff for: lib/tsinfer.h

@@ -164,7 +164,7 @@ typedef struct {
     size_t num_sites;
     size_t max_nodes;
     /* Input LS model rates */
-    unsigned int precision;
+    double likelihood_threshold;
     double *recombination_rate;
     double *mismatch_rate;
     /* The quintuply linked tree */
@@ -207,7 +207,7 @@ int ancestor_builder_finalise(ancestor_builder_t *self);
 
 int ancestor_matcher_alloc(ancestor_matcher_t *self,
     tree_sequence_builder_t *tree_sequence_builder, double *recombination_rate,
-    double *mismatch_rate, unsigned int precision, int flags);
+    double *mismatch_rate, double likelihood_threshold, int flags);
 int ancestor_matcher_free(ancestor_matcher_t *self);
 int ancestor_matcher_find_path(ancestor_matcher_t *self, tsk_id_t start, tsk_id_t end,
     allele_t *haplotype, allele_t *matched_haplotype, size_t *num_output_edges,