Changeset 3412

Timestamp:

Apr 23, 2015, 1:00:30 AM (8 years ago)

Author:

Peter

Message:

throw exception rather than returnining empty string when ID or KEY is missing in header. refs #817

Location:

trunk

Files:

• test/bam_header.cc (modified) (1 diff)
• yat/omic/BamHeader.cc (modified) (2 diffs)

trunk/test/bam_header.cc

@@ -143 +143 @@
     suite.err() << "error: exception: " << e.what() << "\n";
   }
+
+  try {
+    // try calling unknown ID
+    hdr.read_group("banana", "SM");
+    suite.add(false);
+    suite.err() << "read_group(\"banana\", \"SM\") didn't throw\n";
+  }
+  catch (utility::runtime_error& e) {
+    suite.out() << "expected exception with what(): " << e.what() << "\n";
+  }
+
+  try {
+    // try calling unknown key
+    hdr.read_group("foo", "HM");
+    suite.add(false);
+    suite.err() << "read_group(\"foo\", \"HM\") didn't throw\n";
+  }
+  catch (utility::runtime_error& e) {
+    suite.out() << "expected exception with what(): " << e.what() << "\n";
+  }
 #endif
 }

trunk/yat/omic/BamHeader.cc

@@ -26 +26 @@
 #include "yat/utility/Exception.h"
 #include "yat/utility/split.h"
+#include "yat/utility/stl_utility.h"
 
 // we need to include 'sam_header.h' when compiling against libbam
@@ -99 +100 @@
         }
       }
-      if (table.empty())
-        table[""][""]; // to avoid re-parsing
-    }
-    return table[id][key];
+    }
+    strMap2::const_iterator line_table = table.find(id);
+    if (line_table == table.end()) {
+      std::string msg = "@" + type + ": unknown ID: '" + id + "'";
+      throw utility::runtime_error(msg);
+    }
+    strMap::const_iterator it = line_table->second.find(key);
+    if (it == line_table->second.end()) {
+      std::string msg = "@" + type + ": unknown KEY: '" + key + "'";
+      throw utility::runtime_error(msg);
+    }
+    return it->second;
   }