Example #1
0
    @Override
    public void handle(HttpExchange t) throws IOException {

      String fileId = t.getRequestURI().getPath().replaceFirst("/header/", "");
      System.out.println("fileId: " + fileId);
      InputStream is = new FileInputStream("C:\\Users\\vadim\\Downloads\\15496_1#45.cram");
      CramHeader cramHeader = CramIO.readCramHeader(is);

      t.getResponseHeaders().add(HttpHeaders.CONTENT_TYPE, "SAM_HEADER");

      t.getResponseHeaders()
          .add(
              "CRAM_VERSION",
              String.format("%d.%d", cramHeader.getMajorVersion(), cramHeader.getMinorVersion()));
      t.sendResponseHeaders(200, 0);

      ByteArrayOutputStream headerBodyOS = new ByteArrayOutputStream();
      OutputStreamWriter w = new OutputStreamWriter(headerBodyOS);
      new SAMTextHeaderCodec().encode(w, cramHeader.getSamFileHeader());
      try {
        w.close();
      } catch (IOException e) {
        throw new RuntimeException(e);
      }

      OutputStream os = t.getResponseBody();
      os.write(headerBodyOS.toByteArray());
      os.close();
    }
Example #2
0
  public BaiIndexer(InputStream is, File output) throws IOException {
    this.is = new CountingInputStream(is);
    CramHeader cramHeader = CramIO.readCramHeader(this.is);
    samFileHeader = cramHeader.getSamFileHeader();

    indexer = new CRAMIndexer(output, samFileHeader);
  }