Version 2.7.5

Author: hannespetur

src/graph/constructor.cpp

@@ -1579,9 +1579,9 @@ void add_var_record(std::vector<VarRecord> & var_records,
           else
           {
             assert(key == "GT_HAPLOTYPE");
-            auto const val_ul = std::stoul(val_str);
-            ref.anti_events.insert(val_ul);
-            // alt.anti_events.insert(-val_ul);
+            int const val_ul = std::stol(val_str);
+            // ref.anti_events.insert(val_ul);
+            alt.anti_events.insert(-val_ul);
           }
         } // for (auto const & val : values)
       }   // for (auto const & info : infos)

src/graph/haplotype.cpp

@@ -505,11 +505,12 @@ void Haplotype::explain_to_score(std::size_t const pn_index,
 
 #ifndef NDEBUG
   // TODO(h2) THE FOLLOWING DOESNT MAKE SENSE
-  /*assert(!explains.none());
+  assert(!explains.empty());
 
+  /*
   if (explains.none())
     explains.set(); // Flip 'em all, cause they can all explain this read
-    */
+  */
 #endif // NDEBUG
 
   // std::vector<uint16_t> haplotype_errors = find_with_how_many_errors_haplotypes_explain_the_read(cnum);

src/typer/caller.cpp

@@ -56,7 +56,7 @@ namespace
 {
 #ifndef NDEBUG
 std::string const debug_read_name = "HISEQ1:33:H9YY4ADXX:1:2110:2792:58362/2";
-long debug_event_pos{152195561};
+long debug_event_pos{3603668};
 char debug_event_type{'X'};
 std::size_t debug_event_size{1};
 #endif // NDEBUG
@@ -74,6 +74,11 @@ void merge_haplotypes2(std::map<gyper::Event, Thap> & into, std::map<gyper::Even
   // Insert any elements from "from" into "into"
   for (auto from_it = from.begin(); from_it != from.end(); ++from_it)
   {
+#ifndef NDEBUG
+    if (from_it->first.pos == debug_event_pos)
+      gyper::print_log(gyper::log_severity::info, __HERE__, " var ", from_it->first.to_string());
+#endif // NDEBUG
+
     auto insert_p = into.insert(*from_it);
 
     if (insert_p.second)
@@ -82,6 +87,11 @@ void merge_haplotypes2(std::map<gyper::Event, Thap> & into, std::map<gyper::Even
       // nothing needs to be done for "ever_together"
       // go through all events in the newly inserted "always_together" and remove any that have been seen in into
 
+#ifndef NDEBUG
+      if (insert_p.first->first.pos == debug_event_pos)
+        gyper::print_log(gyper::log_severity::info, __HERE__, " new var ", insert_p.first->first.to_string());
+#endif // NDEBUG
+
       gyper::HaplotypeInfo & into_hap_info = insert_p.first->second;
       auto it = into_hap_info.always_together.begin();
 
@@ -131,16 +141,20 @@ void merge_haplotypes2(std::map<gyper::Event, Thap> & into, std::map<gyper::Even
         }
       }
 
-      /*
-      gyper::print_log(gyper::log_severity::info,
-                       __HERE__,
-                       " ",
-                       from_hap_info.always_together.size(),
-                       " ",
-                       into_hap_info.always_together.size(),
-                       " ",
-                       intersection.size());
-      */
+#ifndef NDEBUG
+      if (insert_p.first->first.pos == debug_event_pos)
+      {
+        gyper::print_log(gyper::log_severity::info, __HERE__, " intersection of ", insert_p.first->first.to_string());
+        gyper::print_log(gyper::log_severity::info,
+                         __HERE__,
+                         " ",
+                         from_hap_info.always_together.size(),
+                         " ",
+                         into_hap_info.always_together.size(),
+                         " ",
+                         intersection.size());
+      }
+#endif // NDEBUG
 
       insert_p.first->second.always_together = std::move(intersection);
     }

test/graph/test_constructor.cpp

@@ -530,9 +530,9 @@ TEST_CASE("Construct test graph with anti events (chr10)")
   }
 
   {
-    REQUIRE(var_nodes[0].anti_events.size() == 1);
-    REQUIRE(var_nodes[0].anti_events.count(2) == 1);
-    REQUIRE(var_nodes[1].anti_events.size() == 0);
+    REQUIRE(var_nodes[0].anti_events.size() == 0);
+    REQUIRE(var_nodes[1].anti_events.size() == 1);
+    REQUIRE(var_nodes[1].anti_events.count(-2) == 1);
     REQUIRE(var_nodes[2].anti_events.size() == 0);
     REQUIRE(var_nodes[3].anti_events.size() == 0);
   }
@@ -553,7 +553,7 @@ TEST_CASE("Construct test graph with anti events (chr11)")
 
   {
     REQUIRE(ref_nodes.size() == 2);
-    REQUIRE(var_nodes.size() == 6);
+    REQUIRE(var_nodes.size() == 4);
   }
 
   Options::instance()->add_all_variants = false;

test/index/test_index.cpp

@@ -431,7 +431,7 @@ TEST_CASE("Test index chr10 with parity event")
   REQUIRE(labels[0].variant_id != labels[1].variant_id);
 
   labels = ph_index.get(gyper::to_uint64("AGGGGGGTGGGGGGGGGGGGGGGGGGGGGGGG", 0));
-  REQUIRE(labels.size() == 2);
+  REQUIRE(labels.size() == 0);
 
   labels = ph_index.get(gyper::to_uint64("AGGGGGAGTGGGGGGGGGGGGGGGGGGGGGGG", 0));