// open input files
BamMultiReader reader;
- if (!reader.Open(m_settings->InputFiles, false)) {
- cerr << "Could not open input files" << endl;
- return false;
+ if ( !m_settings->HasInput ) { // don't attempt to open index for stdin
+ if ( !reader.Open(m_settings->InputFiles, false) ) {
+ cerr << "Could not open input files" << endl;
+ return false;
+ }
+ } else {
+ if ( !reader.Open(m_settings->InputFiles, true) ) {
+ cerr << "Could not open input files" << endl;
+ return false;
+ }
}
m_references = reader.GetReferenceData();