log.warn("No output file, writint to STDOUT.");
os = System.out;
}
if (params.encrypt) {
CipherOutputStream_256 cos = new CipherOutputStream_256(os, pass,
128);
os = cos.getCipherOutputStream();
}
CramHeader h = new CramHeader(2, 0, params.bamFile == null ? "STDIN"
: params.bamFile.getName(), samFileReader.getFileHeader());
long offset = ReadWrite.writeCramHeader(h, os);