Beispiel #1
0
  /**
   * Read only header info
   *
   * @return
   */
  public VcfHeader readHeader() {
    // No more header to read?
    if ((nextLine != null) && !nextLine.startsWith("#")) return header;

    try {
      while (ready()) {
        line = readLine();
        if (line == null) return null; // End of file?
        if (!line.startsWith("#")) {
          nextLine = line;
          return header; // End of header?
        }

        header.addLine(line);
      }
    } catch (IOException e) {
      throw new RuntimeException(
          "Error reading file '"
              + fileName
              + "'. Line ignored:\n\tLine ("
              + lineNum
              + "):\t'"
              + line
              + "'");
    }

    return header;
  }
Beispiel #2
0
 /**
  * Parse a line from a VCF file
  *
  * @param line
  * @return
  */
 protected VcfEntry parseVcfLine(String line) {
   try {
     if (line.startsWith("#")) {
       header.addLine(line); // Header?
     } else if ((line.length() > 0) && (!line.startsWith("#")))
       return new VcfEntry(this, line, lineNum, parseNow); // Vcf entry?
   } catch (Throwable t) {
     Gpr.debug("Fatal error reading file '" + fileName + "' (line: " + lineNum + "):\n" + line);
     throw new RuntimeException(t);
   }
   // Could not create a VcfEntry from this line (e.g. header line)
   return null;
 }
Beispiel #3
0
 /**
  * Get sample names
  *
  * @return
  */
 public List<String> getSampleNames() {
   return header.getSampleNames();
 }