Merge pull request #3715 from vgteam/surject-interval-crash

Surject interval crash
vgteam · Aug 13, 2022 · 22ac546 · 22ac546 · adamnovak · Aug 14, 2022
2 parents fd97f17 + 5cbb263
commit 22ac546
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Showing 2 changed files with 15 additions and 9 deletions.
diff --git a/src/subcommand/autoindex_main.cpp b/src/subcommand/autoindex_main.cpp
@@ -142,6 +142,8 @@ int main_autoindex(int argc, char** argv) {
     bool force_phased = false;
     int64_t target_mem_usage = IndexRegistry::get_system_memory() / 2;
 
+    string gfa_name;
+
     int c;
     optind = 2; // force optind past command positional argument
     while (true) {
@@ -215,12 +217,7 @@ int main_autoindex(int argc, char** argv) {
                 registry.provide("Insertion Sequence FASTA", optarg);
                 break;
             case 'g':
-                if (IndexRegistry::gfa_has_haplotypes(optarg)) {
-                    registry.provide("Reference GFA w/ Haplotypes", optarg);
-                }
-                else {
-                    registry.provide("Reference GFA", optarg);
-                }
+                gfa_name = optarg;
                 break;
             case 'x':
                 registry.provide("GTF/GFF", optarg);
@@ -312,6 +309,15 @@ int main_autoindex(int argc, char** argv) {
             }
         }
     }
+
+    if (!gfa_name.empty()) {
+        if (IndexRegistry::gfa_has_haplotypes(gfa_name)) {
+            registry.provide("Reference GFA w/ Haplotypes", gfa_name);
+        }
+        else {
+            registry.provide("Reference GFA", gfa_name);
+        }
+    }
 
     if (print_dot) {
         // don't index, just visualize the plan

diff --git a/src/surjector.cpp b/src/surjector.cpp
@@ -3802,7 +3802,7 @@ using namespace std;
 
             size_t right_overhang = no_right_expansion ? 0 : (get_aligner()->longest_detectable_gap(source, path_chunk.first.second)
                                                               + (source.sequence().end() - path_chunk.first.second));
-
+                        
             const Position& first_pos = path_chunk.second.mapping(0).position();
             if (rev_strand) {
                 size_t path_offset = (graph->get_position_of_step(ref_chunk.first)
@@ -3818,7 +3818,7 @@ using namespace std;
                     interval.first = 0;
                 }
                 else {
-                    interval.first = min(interval.first, path_offset - left_overhang);
+                    interval.first = min(min(interval.first, path_offset - left_overhang), path_length - 1);
                 }
             }
 
@@ -3834,7 +3834,7 @@ using namespace std;
                     interval.first = 0;
                 }
                 else {
-                    interval.first = min(interval.first, path_offset - right_overhang);
+                    interval.first = min(min(interval.first, path_offset - right_overhang), path_length - 1);
                 }
             }
             else {