Method getHeaderLines

src/main/java/com/rtg/vcf/VcfMerge.java:145–173

(CFlags flags)

  }

  static Collection<String> getHeaderLines(CFlags flags) throws IOException {
    final List<String> extraHeaderLines = new ArrayList<>();
    if (flags.isSet(ADD_HEADER_FLAG)) {
      for (final Object o : flags.getValues(ADD_HEADER_FLAG)) {
        final String lineOrFile = (String) o;
        if (lineOrFile.length() > 0) {
          if (VcfHeader.isMetaLine(lineOrFile)) {
            extraHeaderLines.add(lineOrFile);
          } else if (new File(lineOrFile).exists()) {
            try (BufferedReader r = new BufferedReader(new InputStreamReader(FileUtils.createInputStream(new File(lineOrFile), false)))) {
              String line;
              while ((line = r.readLine()) != null) {
                if (line.length() > 0) {
                  if (VcfHeader.isMetaLine(line)) {
                    extraHeaderLines.add(line);
                  } else {
                    throw new VcfFormatException("In additional header file " + lineOrFile + ", line '" + line + "', doesn't look like a VCF header line");
                  }
                }
              }
            }
          } else {
            throw new VcfFormatException("Additional header argument '" + lineOrFile + "', doesn't look like a VCF header line or a file");
          }
        }
      }
    }
    return extraHeaderLines;
  }

  @Override
  protected int mainExec(final OutputStream out, final PrintStream err) throws IOException {