Examples of SAMTextWriter

public class SamAlignmentEncoder implements FeatureEncoder<PicardAlignment> {


    private boolean headerSet = false;


    public Map<String, Object> encodeAll(OutputStream stream, Iterator<? extends PicardAlignment> alignments) {
        SAMFileWriterImpl writer = new SAMTextWriter(stream);
        while (alignments.hasNext()) {
            PicardAlignment samAl = alignments.next();
            if (!headerSet) {
                writer.setSortOrder(SAMFileHeader.SortOrder.unsorted, true);
                writer.setHeader(samAl.getRecord().getHeader());
                headerSet = true;
            }
            writer.addAlignment(samAl.getRecord());
        }
        writer.close();
        return null;
    }

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;
    }

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.

Examples of SAMTextWriter

Examples of htsjdk.samtools.SAMTextWriter

Examples of net.sf.samtools.SAMTextWriter