Package net.sf.cram.io

Examples of net.sf.cram.io.CountingInputStream

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            params.cramFile), pass, 1, 128);
      }
    }

    long offset = 0;
    CountingInputStream cis = new CountingInputStream(is);
    CramHeader cramHeader = ReadWrite.readCramHeader(cis);
    offset = cis.getCount();

    SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
    samFileWriterFactory.setAsyncOutputBufferSize(10000);
    samFileWriterFactory.setCreateIndex(false);
    samFileWriterFactory.setCreateMd5File(false);
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  public CountingInputStream is;
  public SAMFileHeader samFileHeader;
  public CRAMIndexer indexer;

  public BaiIndexer(InputStream is, SAMFileHeader samFileHeader, File output) {
    this.is = new CountingInputStream(is);
    this.samFileHeader = samFileHeader;

    indexer = new CRAMIndexer(output, samFileHeader);
  }
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    indexer = new CRAMIndexer(output, samFileHeader);
  }

  public BaiIndexer(InputStream is, File output) throws IOException {
    this.is = new CountingInputStream(is);
    CramHeader cramHeader = ReadWrite.readCramHeader(this.is);
    samFileHeader = cramHeader.samFileHeader;

    indexer = new CRAMIndexer(output, samFileHeader);
  }
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  private SAMFileHeader samFileHeader;
  private CramIndex index;

  public CraiIndexer(InputStream is, File output)
      throws FileNotFoundException, IOException {
    this.is = new CountingInputStream(is);
    CramHeader cramHeader = ReadWrite.readCramHeader(this.is);
    samFileHeader = cramHeader.samFileHeader;

    index = new CramIndex(new GZIPOutputStream(new BufferedOutputStream(
        new FileOutputStream(output))));
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Related Classes of net.sf.cram.io.CountingInputStream

  • net.sf.cram.Cram2Bam
  • net.sf.cram.index.BaiIndexer
  • net.sf.cram.index.CraiIndexer
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