public void prepareWalker(Walker walker, SAMFileReader.ValidationStringency strictnessLevel) {
for (Map.Entry<ArgumentSource, Object> io : inputs.entrySet()) {
ArgumentSource targetField = io.getKey();
Object targetValue = io.getValue();
// Ghastly hack: reaches in and finishes building out the SAMFileReader.
// TODO: Generalize this, and move it to its own initialization step.
if (targetValue instanceof SAMFileReaderBuilder) {
SAMFileReaderBuilder builder = (SAMFileReaderBuilder) targetValue;
builder.setValidationStringency(strictnessLevel);
targetValue = builder.build();
}
JVMUtils.setFieldValue(targetField.field, walker, targetValue);
}
}
/**
* Install an OutputStreamStub into the given fieldName of the given walker.
*
* @param walker Walker into which to inject the field name.
* @param fieldName Name of the field into which to inject the stub.
*/
private void installStub(Walker walker, String fieldName, OutputStream outputStream) {
Field field = JVMUtils.findField(walker.getClass(), fieldName);
JVMUtils.setFieldValue(field, walker, outputStream);
}