String pathToBamFile = commandLine.getOptionValue("i");
SAMFileReader reader = new SAMFileReader(new File(pathToBamFile));
// Init reference
String pathToRef = commandLine.getOptionValue("r");
IndexedFastaSequenceFile refIndex = new IndexedFastaSequenceFile(new File(pathToRef));
int numberOfProblematicReads = 0;
int numReads = 0;
SAMRecordIterator iter = reader.iterator();