public void prepareWalker( Walker walker, 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 SameReader. // TODO: Generalize this, and move it to its own initialization step. if( targetValue instanceof SAMReaderBuilder) { SAMReaderBuilder builder = (SAMReaderBuilder)targetValue; builder.setValidationStringency(strictnessLevel); targetValue = builder.build(); } JVMUtils.setFieldValue( targetField.field, walker, targetValue ); } }