Examples of BAMFileWriter

Examples of net.sf.samtools.BAMFileWriter

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      }
    } else if (params.outputFile == null) {
      OutputStream os = new BufferedOutputStream(System.out);
      if (params.outputBAM) {
        BAMFileWriter ret = new BAMFileWriter(os, null);
        ret.setSortOrder(cramHeader.samFileHeader.getSortOrder(), true);
        ret.setHeader(cramHeader.samFileHeader);
        writer = ret;
      } else {
        writer = Utils.createSAMTextWriter(samFileWriterFactory, os,
            cramHeader.samFileHeader, params.printSAMHeader);
      }
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Examples of net.sf.samtools.BAMFileWriter

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            params.outFile);
    else if (!params.samFormat) {
      // hack to write BAM format to stdout:
      File file = File.createTempFile("bam", null);
      file.deleteOnExit();
      BAMFileWriter bamWriter = new BAMFileWriter(System.out, file);
      header.setSortOrder(SortOrder.coordinate);
      bamWriter.setHeader(header);
      writer = bamWriter;
    }

    else {
      writer = Utils.createSAMTextWriter(null, System.out, header,
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