- BamReader* reader = OpenReader(filename);
- if ( reader == 0 ) continue;
-
- // store reader with new alignment
- m_readers.push_back( make_pair(reader, new BamAlignment) );
+ bool openedOk = false;
+ ReaderAlignment ra = OpenReader(filename, &openedOk);
+ if ( openedOk ) {
+ m_readers.push_back(ra); // store reader/alignment in local list
+ m_alignments->Add(ra); // add reader/alignment to sorting cache
+ }