// opens the BAM files without checking for indexes
BamMultiReader reader;
- reader.Open(m_settings->InputFiles, false);
+ reader.Open(m_settings->InputFiles, false, true);
// retrieve header & reference dictionary info
std::string mergedHeader = reader.GetHeaderText();
// store alignments to output file
BamAlignment bAlignment;
- while (reader.GetNextAlignment(bAlignment)) {
+ while (reader.GetNextAlignmentCore(bAlignment)) {
writer.SaveAlignment(bAlignment);
}
-
+
// clean & exit
reader.Close();
writer.Close();