}
private void standardReheader(final SAMFileHeader replacementHeader) {
final SAMFileReader recordReader = new SAMFileReader(INPUT);
if (replacementHeader.getSortOrder() != recordReader.getFileHeader().getSortOrder()) {
throw new PicardException("Sort orders of INPUT (" + recordReader.getFileHeader().getSortOrder().name() +
") and HEADER (" + replacementHeader.getSortOrder().name() + ") do not agree.");
}
final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(replacementHeader, true, OUTPUT);
final ProgressLogger progress = new ProgressLogger(Log.getInstance(ReplaceSamHeader.class));