995d2d2c682b26c07907090cc269a975811ce15b,public/java/src/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java,NWaySAMFileWriter,addWriter,#SAMReaderID#String#SAMFileHeader.SortOrder#boolean#boolean#boolean#SAMProgramRecord#,139

Before Change


    private void addWriter(SAMReaderID id , String outName, SAMFileHeader.SortOrder order, boolean presorted,
                           boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord programRecord) {
        File f = new File(outName);
        SAMFileHeader header = toolkit.getSAMFileHeader(id).clone();
        header.setSortOrder(order);

        if ( programRecord != null )  {

After Change


    private void addWriter(SAMReaderID id , String outName, SAMFileHeader.SortOrder order, boolean presorted,
                           boolean indexOnTheFly, boolean generateMD5, SAMProgramRecord programRecord) {
        File f = new File(outName);
        SAMFileHeader header = Utils.setupWriter(toolkit, toolkit.getSAMFileHeader(id), KEEP_ALL_PG_RECORDS, programRecord);
        SAMFileWriterFactory factory = new SAMFileWriterFactory();
        factory.setCreateIndex(indexOnTheFly);
        factory.setCreateMd5File(generateMD5);