// initialize defined properties & user-specified filters
// quit if failed
- if ( !SetupFilters() ) return 1;
+ if ( !SetupFilters() ) return false;
// open reader without index
BamMultiReader reader;
- if ( !reader.Open(m_settings->InputFiles, false, true) ) {
+ if ( !reader.Open(m_settings->InputFiles, false, false) ) {
cerr << "Could not open input files for reading." << endl;
return false;
}
// attempt to re-open reader with index files
reader.Close();
- bool openedOK = reader.Open(m_settings->InputFiles, true, true );
+ bool openedOK = reader.Open(m_settings->InputFiles, true, false );
// if error
if ( !openedOK ) {
cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
- return 1;
+ return false;
}
// if index data available, we can use SetRegion
if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
cerr << "ERROR: Region requested, but could not set BamReader region to REGION: " << m_settings->Region << " Aborting." << endl;
reader.Close();
- return 1;
+ return false;
}
// everything checks out, just iterate through specified region, filtering alignments
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();
- return 1;
+ return false;
}
}
// clean up & exit
reader.Close();
writer.Close();
- return 0;
+ return true;
}
bool FilterTool::FilterToolPrivate::SetupFilters(void) {