message: allow calling on N-matching bases
diff: @@ -134,10 +134,10 @@ int main (int argc, char *argv[]) {
  nonCalls.clear();
  }
  - // don't process non-ATGC's in the reference
  + // don't process non-ATGCN's in the reference
  string cb = parser->currentReferenceBaseString();
  - if (cb != "A" && cb != "T" && cb != "C" && cb != "G") {
  - DEBUG2("current reference base is N");
  + if (cb != "A" && cb != "T" && cb != "C" && cb != "G" && cb != "N") {
  + DEBUG2("current reference base is not in { A T G C N }");
  continue;
  }
  