public boolean fixHeaderInFile(File cramFile) throws IOException, MD5MismatchError { FileInputStream fis = new FileInputStream(cramFile); CramHeader cramHeader = CramIO.readCramHeader(fis); fixSequences(cramHeader.getSamFileHeader().getSequenceDictionary().getSequences()); String cmd = "fixheader"; String version = getClass().getPackage().getImplementationVersion(); addPG(cramHeader.getSamFileHeader(), "cramtools", cmd, version); CramHeader newHeader = cramHeader.clone(); return CramIO.replaceCramHeader(cramFile, newHeader); }
fixer.addCramtoolsPG(cramHeader.getSamFileHeader()); CramHeader newHeader = cramHeader.clone();