diff --git a/ehunter/io/ParameterLoading.cpp b/ehunter/io/ParameterLoading.cpp
index 6087605..2c11481 100644
--- a/ehunter/io/ParameterLoading.cpp
+++ b/ehunter/io/ParameterLoading.cpp
@@ -163,11 +163,11 @@ static void assertPathToExistingFile(const string& pathEncoding)
 
 static void assertIndexExists(const string& htsFilePath)
 {
-    const vector<string> kPossibleIndexExtensions = { ".bai", ".csi", ".crai" };
+    const vector<string> kPossibleIndexExtensions = { ".bai", ".bam.bai", ".csi", ".bam.csi", ".cram.csi", ".crai", ".cram.crai" };
 
     for (const string& indexExtension : kPossibleIndexExtensions)
     {
-        if (fs::exists(htsFilePath + indexExtension))
+        if (fs::exists(htsFilePath.substr(0, htsFilePath.find_last_of(".")) + indexExtension))
         {
             return;
         }
diff --git a/ehunter/thirdparty/graph-tools-master-0cd9399/src/graphcore/GraphCoordinates.cpp b/ehunter/thirdparty/graph-tools-master-0cd9399/src/graphcore/GraphCoordinates.cpp
index 2550eda..f90eddc 100644
--- a/ehunter/thirdparty/graph-tools-master-0cd9399/src/graphcore/GraphCoordinates.cpp
+++ b/ehunter/thirdparty/graph-tools-master-0cd9399/src/graphcore/GraphCoordinates.cpp
@@ -22,6 +22,8 @@
 #include "graphutils/PairHashing.hh"
 
 #include <cassert>
+#include <stdexcept>
+#include <limits>
 
 namespace graphtools
 {