Merge pull request #1132 from castedo/pr/vargen_samples

add convenience data member samples for vargen

Author: mergify[bot]

c/tskit/genotypes.c

@@ -159,6 +159,7 @@ tsk_vargen_init(tsk_vargen_t *self, const tsk_treeseq_t *tree_sequence,
     memset(self, 0, sizeof(tsk_vargen_t));
 
     if (samples == NULL) {
+        self->samples = tsk_treeseq_get_samples(tree_sequence);
         self->num_samples = tsk_treeseq_get_num_samples(tree_sequence);
         self->sample_index_map = tsk_treeseq_get_sample_index_map(tree_sequence);
         num_samples_alloc = self->num_samples;
@@ -171,6 +172,7 @@ tsk_vargen_init(tsk_vargen_t *self, const tsk_treeseq_t *tree_sequence,
         if (ret != 0) {
             goto out;
         }
+        self->samples = samples;
         self->num_samples = num_samples;
         self->sample_index_map = self->alt_sample_index_map;
     }

c/tskit/genotypes.h

@@ -52,9 +52,8 @@ typedef struct {
     size_t num_samples;
     size_t num_sites;
     const tsk_treeseq_t *tree_sequence;
-    const tsk_id_t *sample_index_map;
-    tsk_id_t *alt_samples;
-    tsk_id_t *alt_sample_index_map;
+    const tsk_id_t *samples;          /* samples being used */
+    const tsk_id_t *sample_index_map; /* reverse index map being used */
     bool user_alleles;
     char *user_alleles_mem;
     size_t tree_site_index;
@@ -63,6 +62,9 @@ typedef struct {
     tsk_tree_t tree;
     tsk_flags_t options;
     tsk_variant_t variant;
+    // private: the following data members are not intended to be used externally
+    tsk_id_t *alt_samples; /* alternative subset of samples to use */
+    tsk_id_t *alt_sample_index_map;
 } tsk_vargen_t;
 
 int tsk_vargen_init(tsk_vargen_t *self, const tsk_treeseq_t *tree_sequence,