Fix segfault in VariantReader on non-existent file

broadinstitute · Oct 29, 2014 · 7fee5cc · 7fee5cc
1 parent a2a79b6
commit 7fee5cc
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diff --git a/gamgee/variant_reader.h b/gamgee/variant_reader.h
@@ -14,6 +14,7 @@
 #include <fstream>
 #include <algorithm>
 #include <memory>
+#include <stdexcept>
 
 
 namespace gamgee {
@@ -163,6 +164,9 @@ class VariantReader {
    */
   void init_reader (const std::string& filename) {
     auto* file_ptr = bcf_open(filename.empty() ? "-" : filename.c_str(), "r");
+    if ( file_ptr == nullptr ) {
+      throw std::invalid_argument{std::string{"Could not open file "} + filename};
+    }
     m_variant_file_ptr = utils::make_shared_hts_file (file_ptr);
     m_variant_header_ptr = utils::make_shared_variant_header (bcf_hdr_read (file_ptr));
   }

diff --git a/test/variant_reader_test.cpp b/test/variant_reader_test.cpp
@@ -14,6 +14,7 @@
 #include <boost/test/unit_test.hpp>
 #include <boost/algorithm/string/join.hpp>
 #include <boost/iterator/zip_iterator.hpp>
+#include <stdexcept>
 
 using namespace std;
 using namespace gamgee;
@@ -1340,3 +1341,7 @@ BOOST_AUTO_TEST_CASE( synced_variant_iterator_move_test ) {
     BOOST_CHECK_EQUAL(record0[0].alignment_start(), moved_record[0].alignment_start());
   }
 }
+
+BOOST_AUTO_TEST_CASE( variant_reader_nonexistent_file ) {
+  BOOST_CHECK_THROW(SingleVariantReader{"foo/bar/nonexistent.vcf"}, invalid_argument);
+}