diff --git a/reach/README.md b/reach/README.md
index 39a41185..8fb449f9 100644
--- a/reach/README.md
+++ b/reach/README.md
@@ -85,9 +85,6 @@ stdout if no path was given.
 Under `lib/`:
 - json.hpp
   + open-source (MIT) JSON library from https://github.com/nlohmann/json
-- cache.hpp
-  + templated helper functions for reading/writing data structures
-    (vector, unordered_set, unordered_map) to/from disk
 - facts.hpp, facts.cpp
   + in-memory representation of fact databases, and loading from .facts files
   + defns related to dlsym loaded symbol logs from dynamic analysis
diff --git a/reach/lib/binary_heap.hpp b/reach/lib/binary_heap.hpp
index 74b78695..57597582 100644
--- a/reach/lib/binary_heap.hpp
+++ b/reach/lib/binary_heap.hpp
@@ -8,6 +8,11 @@
 // Use this instead of std::priority_queue for fast 'contains' and
 // 'decrease_key' operations.
 
+// 0-indexed heap:
+//        0
+//    1       2
+//  3   4   5   6
+
 #pragma once
 
 #include <stdexcept>
@@ -31,11 +36,18 @@ class binary_heap {
 
   // Extract the minimum element from the heap.
   std::pair<K, V> extract() {
+    if (_heap.empty()) {
+      throw std::out_of_range("extract on empty heap");
+    }
     const auto root = this->_heap.front();
-    this->_heap[0] = this->_heap.back();
-    this->_heap.pop_back();
     this->_ixs.erase(root.first);
+    if (this->_heap.size() == 1) {
+      this->_heap.pop_back();
+      return root;
+    }
+    this->_heap[0] = this->_heap.back();
     this->_ixs[this->_heap[0].first] = 0;
+    this->_heap.pop_back();
     this->_heapify_down(0);
     return root;
   }
@@ -69,7 +81,7 @@ class binary_heap {
   // Heapify up at index [i].
   void _heapify_up(size_t i) {
     if (i > 0) {
-      size_t parent_i = i / 2;
+      size_t parent_i = (i - 1) / 2;
       if (this->_heap[i].second < this->_heap[parent_i].second) {
         this->_swap(i, parent_i);
         this->_heapify_up(parent_i);
@@ -79,8 +91,8 @@ class binary_heap {
 
   // Heapify down at index [i].
   void _heapify_down(size_t i) {
-    size_t left_i = 2 * i;
-    size_t right_i = 2 * i + 1;
+    size_t left_i = 2 * i + 1;
+    size_t right_i = 2 * i + 2;
 
     size_t smallest = i;
     if (left_i < this->_heap.size() &&
diff --git a/reach/src/main.cpp b/reach/src/main.cpp
index 05429bcd..4124763a 100644
--- a/reach/src/main.cpp
+++ b/reach/src/main.cpp
@@ -132,8 +132,6 @@ int main(int argc, char* argv[]) {
     .flag();
   program.add_argument("-ds", "--dlsym-log")
     .help("path to file containing dlsym log of loaded symbols");
-  program.add_argument("-o", "--output")
-    .help("JSON output path");
   program.add_argument("-g", "--graph")
     .help("graph type (\"simple\", \"cfg\", or \"call\"). Default \"cfg\"");
   program.add_argument("-n", "--num-paths")