- writer.Open(m_settings->OutputFilename, headerText, references, writeUncompressed);
-
+ if ( !writer.Open(m_settings->OutputFilename, headerText, references, writeUncompressed) ) {
+ cerr << "ERROR: Could not open BamWriter." << endl;
+ reader.Close();
+ return 1;
+ }
+
+ // if user specified a REGION constraint, attempt to parse REGION string
+ BamRegion region;
+ if ( m_settings->HasRegion && !Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
+ cerr << "ERROR: Could not parse REGION: " << m_settings->Region << endl;
+ cerr << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
+ reader.Close();
+ writer.Close();
+ return 1;
+ }
+