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);