Package net.sf.samtools

Examples of net.sf.samtools.SAMTextWriter


        factoryOrNull = new SAMFileWriterFactory();
      writer = factoryOrNull.makeSAMWriter(header, true, os);
    } else {
      SwapOutputStream sos = new SwapOutputStream();

      final SAMTextWriter ret = new SAMTextWriter(sos);
      ret.setSortOrder(header.getSortOrder(), true);
      ret.setHeader(header);
      ret.getWriter().flush();

      writer = ret;

      sos.delegate = os;
    }
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