diff --git a/.vscode/c_cpp_properties.json b/.vscode/c_cpp_properties.json
index c982100..68f8382 100644
--- a/.vscode/c_cpp_properties.json
+++ b/.vscode/c_cpp_properties.json
@@ -3,21 +3,37 @@
         {
             "name": "Linux",
             "includePath": [
-              "/usr/include",
-              "/usr/lib/syslinux/com32/include",
-              "/usr/lib/gcc/x86_64-linux-gnu/4.8/include",
-              "/usr/lib/syslinux/com32/include",
-              "/usr/lib/jvm/java-8-openjdk-amd64/include",
-              "/usr/lib/jvm/java-7-openjdk-amd64/include",
-              "/usr/src/linux-headers-4.2.0-27/arch/x86/include",
-              "/usr/src/linux-headers-4.2.0-27/include",
-              "/usr/src/linux-headers-4.2.0-27-generic/arch/x86/include",
-              "/usr/src/linux-headers-4.2.0-27-generic/include"
+                "/usr/include",
+                "/usr/lib/syslinux/com32/include",
+                "/usr/lib/gcc/x86_64-linux-gnu/4.8/include",
+                "/usr/lib/syslinux/com32/include",
+                "/usr/lib/jvm/java-8-openjdk-amd64/include",
+                "/usr/lib/jvm/java-7-openjdk-amd64/include",
+                "/usr/src/linux-headers-4.2.0-27/arch/x86/include",
+                "/usr/src/linux-headers-4.2.0-27/include",
+                "/usr/src/linux-headers-4.2.0-27-generic/arch/x86/include",
+                "/usr/src/linux-headers-4.2.0-27-generic/include",
+                "${workspaceRoot}"
             ],
-            "browse" : {
-                "limitSymbolsToIncludedHeaders" : true,
-                "databaseFilename" : ""
-            }
+            "browse": {
+                "limitSymbolsToIncludedHeaders": true,
+                "databaseFilename": "",
+                "path": [
+                    "/usr/include",
+                    "/usr/lib/syslinux/com32/include",
+                    "/usr/lib/gcc/x86_64-linux-gnu/4.8/include",
+                    "/usr/lib/syslinux/com32/include",
+                    "/usr/lib/jvm/java-8-openjdk-amd64/include",
+                    "/usr/lib/jvm/java-7-openjdk-amd64/include",
+                    "/usr/src/linux-headers-4.2.0-27/arch/x86/include",
+                    "/usr/src/linux-headers-4.2.0-27/include",
+                    "/usr/src/linux-headers-4.2.0-27-generic/arch/x86/include",
+                    "/usr/src/linux-headers-4.2.0-27-generic/include",
+                    "${workspaceRoot}"
+                ]
+            },
+            "intelliSenseMode": "clang-x64"
         }
-    ]
-}
+    ],
+    "version": 2
+}
\ No newline at end of file
diff --git a/.vscode/settings.json b/.vscode/settings.json
index ee357d9..15898fb 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -16,8 +16,10 @@
     }
 ,
 "files.associations": {
-  "SConstruct": "python",
-  "*.cu": "c",
-  "*.cuh": "c"
+    "SConstruct": "python",
+    "*.cu": "c",
+    "*.cuh": "c",
+    "log.h": "c",
+    "bw_io.h": "c"
 }
 }
\ No newline at end of file
diff --git a/src/hpg-aligner.c b/src/hpg-aligner.c
index 093e325..928b676 100755
--- a/src/hpg-aligner.c
+++ b/src/hpg-aligner.c
@@ -92,7 +92,8 @@ int main(int argc, char* argv[]) {
   argc -= 1;
   argv += 1;
 
-  if (strcmp(command, "bs") != 0) {
+  if (strcmp(command, "bs") != 0 ||
+      strcmp(command, "build-index") != 0) {
     LOG_FATAL("Command unknown.\nValid commands are:\n \
     \tbs: to map BS sequences\n \
     \tbuild-index: to create the genome index.\n \