Merge pull request #7 from mobinasri/dev-0.2.0

Dev 0.2.0
mobinasri · May 3, 2023 · 9ee387c · 9ee387c
2 parents dac29a7 + 1da064d
commit 9ee387c
Showing 1 changed file with 6 additions and 2 deletions.
diff --git a/programs/submodules/ptVariant/ptVariant.c b/programs/submodules/ptVariant/ptVariant.c
@@ -953,9 +953,13 @@ stList *ptVariant_subset_stList(stList *variants, stHash *blocks_per_contig) {
         if (strcmp(contig, variant->contig) != 0) {
             strcpy(contig, variant->contig);
             blocks = stHash_search(blocks_per_contig, contig);
-            j = 0;
-            block = stList_get(blocks, j);
+            // handle the case when the whole contig is not in the bed file
+            if (blocks != NULL) {
+                j = 0;
+                block = stList_get(blocks, j);
+            }
         }
+        if (blocks == NULL) continue;
         while (block->rfe < variant->pos && j < stList_length(blocks) - 1) {
             j += 1;
             block = stList_get(blocks, j);