SAMFileWriterFactory.setDefaultCreateMd5File(CREATE_MD5_FILE);
SAMFileWriterFactory.setDefaultCreateMd5File(CREATE_MD5_FILE);
outHeader.setSortOrder(SORT_ORDER); SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(CREATE_INDEX); SAMFileWriterFactory.setDefaultCreateMd5File(CREATE_MD5_FILE); final SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader, false, OUTPUT);
outHeader.setSortOrder(SORT_ORDER); SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(CREATE_INDEX); SAMFileWriterFactory.setDefaultCreateMd5File(CREATE_MD5_FILE); final SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader, false, OUTPUT);