added warning for duplicate @RG tag in header

diff --git a/BamMultiReader.cpp b/BamMultiReader.cpp
index 92911c90da8793a0a86bed63b9ba49ddce137009..e284eca3c6eeabcc30b5026b7f3ed8a40a7acc61 100644 (file)
--- a/BamMultiReader.cpp
+++ b/BamMultiReader.cpp
@@ -249,6 +249,8 @@ const string BamMultiReader::GetHeaderText(void) const {
                     mergedHeader.append(headerLine.c_str() );
                     mergedHeader.append(1, '\n');
                     readGroups[readGroup] = true;
+                } else {
+                    cerr << "WARNING: duplicate @RG tag entry in BAM header " << readGroup << endl;
                 }
             }