return pair;
}
private Pair<BasicFeatureSource, SAMSequenceDictionary> createBasicFeatureSourceNoAssumedIndex(Class targetClass, String name, File inputFile) {
logger.info("Attempting to blindly load " + inputFile + " as a tabix indexed file");
try {
<BUG>return new Pair<BasicFeatureSource, SAMSequenceDictionary>(new BasicFeatureSource(inputFile.getAbsolutePath(), createCodec(targetClass, name)),null);
</BUG>
} catch (IOException e) {
throw new StingException("Unable to create feature reader from file " + inputFile);
}

return pair;
}
private Pair<BasicFeatureSource, SAMSequenceDictionary> createBasicFeatureSourceNoAssumedIndex(Class targetClass, String name, File inputFile) {
logger.info("Attempting to blindly load " + inputFile + " as a tabix indexed file");
try {
return new Pair<BasicFeatureSource, SAMSequenceDictionary>(BasicFeatureSource.getFeatureSource(inputFile.getAbsolutePath(), createCodec(targetClass, name)),null);
} catch (IOException e) {
throw new StingException("Unable to create feature reader from file " + inputFile);
