Ejemplo n.º 1
0
  protected void readAlignments(BufferedReader stdInput, InputStream errorStream)
      throws IOException {
    String outLine;
    SAMAlignmentReader alignmentReader = new SAMAlignmentReader();
    while ((outLine = stdInput.readLine()) != null) {
      if (logger.isDebugEnabled()) {
        logger.debug("LINE: " + outLine);
      }
      if (outLine.startsWith("@")) {
        logger.debug("SAM HEADER LINE: " + outLine);
        continue;
      }

      String readPairId = outLine.substring(0, outLine.indexOf('\t'));
      if (readPairId.endsWith("/1") || readPairId.endsWith("/2")) {
        readPairId = readPairId.substring(0, readPairId.length() - 2);
      }
      AlignmentRecord alignment = alignmentReader.parseRecord(outLine);

      if (!alignment.isMapped()) {
        continue;
      }

      getOutput().collect(new Text(readPairId), new Text(outLine));
    }

    String errLine;
    BufferedReader errorReader = new BufferedReader(new InputStreamReader(errorStream));
    while ((errLine = errorReader.readLine()) != null) {
      logger.error("ERROR: " + errLine);
    }
  }
Ejemplo n.º 2
0
 public final void writeASCII(String s) throws IOException {
   if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
   OutputStream os = getOutputStream();
   synchronized (os) {
     if (Defines.DEBUG && CAT.isDebugEnabled()) CAT.debug("C: " + s);
     os.write(s.getBytes("ASCII"));
     os.write((byte) 13);
     os.write((byte) 10);
     os.flush();
   }
 }
Ejemplo n.º 3
0
  public final String readCommand(byte[] b)
      throws IOException, InterruptedException, MessagingNetworkException {
    InputStream is = getInputStream();
    synchronized (is) {
      long abortTime =
          System.currentTimeMillis() + 1000 * MSNMessagingNetwork.REQPARAM_SOCKET_TIMEOUT_SECONDS;
      int ofs = 0;
      boolean d = false;
      for (; ; ) {
        if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
        int by = is.read();
        if (by == -1) throw new IOException("unexpected EOF");
        if (by == 10 && d) break;
        d = (by == 13);
        if (ofs < b.length) {
          b[ofs++] = (byte) by;
        }
        if (System.currentTimeMillis() > abortTime) throw new IOException("connection timed out");
        /*
        if (len >= buffer.length)
        {
          ...
          return ...;
        }
        int pos = findCRLF();
        if (pos != -1) break;
        fill(is, abortTime);
        */
      }
      if (b[ofs - 1] == 13) --ofs;

      String line = new String(b, 0, ofs, "ASCII");

      if (StringUtil.startsWith(line, "MSG")) {
        StringTokenizer st = new StringTokenizer(line);
        String len_s = null;
        while (st.hasMoreTokens()) {
          len_s = st.nextToken();
        }
        if (len_s == null) throw new AssertException("len_s is null");
        int len;
        try {
          len = Integer.parseInt(len_s);
        } catch (NumberFormatException ex) {
          ServerConnection.throwProtocolViolated("MSG length must be int");
          len = 0;
        }
        String msg = readMSG(len);
        line = line + "\r\n" + msg;
      }
      if (Defines.DEBUG && CAT.isDebugEnabled()) CAT.debug("S: " + line);
      return line;
    }
  }
Ejemplo n.º 4
0
 /**
  * UTF byte count is appended to the asciiPrefix, then UTF bytes are appended to the result; the
  * final result is sent.
  */
 public final void writeMSG(String asciiPrefix, String msgBody) throws IOException {
   if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
   OutputStream os = getOutputStream();
   synchronized (os) {
     byte[] utfBytes = msgBody.getBytes("UTF-8");
     asciiPrefix = asciiPrefix + ' ' + utfBytes.length;
     if (Defines.DEBUG && CAT.isDebugEnabled()) CAT.debug("C: " + asciiPrefix + "\r\n" + msgBody);
     os.write(asciiPrefix.getBytes("ASCII"));
     os.write((byte) 13);
     os.write((byte) 10);
     os.write(utfBytes);
     os.flush();
   }
 }