Esempio n. 1
0
  /**
   * Generates a BAM index file from an input BAM file
   *
   * @param reader SAMFileReader for input BAM file
   * @param output File for output index file
   */
  public static void createIndex(SAMFileReader reader, File output, Log log) {

    BAMIndexer indexer = new BAMIndexer(output, reader.getFileHeader());

    reader.enableFileSource(true);
    int totalRecords = 0;

    // create and write the content
    for (SAMRecord rec : reader) {
      if (++totalRecords % 1000000 == 0) {
        if (null != log) log.info(totalRecords + " reads processed ...");
      }
      indexer.processAlignment(rec);
    }
    indexer.finish();
  }
Esempio n. 2
0
  /**
   * Main method for the program. Checks that all input files are present and readable and that the
   * output file can be written to. Then iterates through all the records generating a BAM Index,
   * then writes the bai file.
   */
  protected int doWork() {

    try {
      inputUrl = new URL(INPUT);
    } catch (java.net.MalformedURLException e) {
      inputFile = new File(INPUT);
    }

    // set default output file - input-file.bai
    if (OUTPUT == null) {

      final String baseFileName;
      if (inputUrl != null) {
        String path = inputUrl.getPath();
        int lastSlash = path.lastIndexOf("/");
        baseFileName = path.substring(lastSlash + 1, path.length());
      } else {
        baseFileName = inputFile.getAbsolutePath();
      }

      if (baseFileName.endsWith(BamFileIoUtils.BAM_FILE_EXTENSION)) {

        final int index = baseFileName.lastIndexOf(".");
        OUTPUT = new File(baseFileName.substring(0, index) + BAMIndex.BAMIndexSuffix);

      } else {
        OUTPUT = new File(baseFileName + BAMIndex.BAMIndexSuffix);
      }
    }

    IOUtil.assertFileIsWritable(OUTPUT);
    final SAMFileReader bam;

    if (inputUrl != null) {
      // remote input
      bam = new SAMFileReader(inputUrl, null, false);
    } else {
      // input from a normal file
      IOUtil.assertFileIsReadable(inputFile);
      bam = new SAMFileReader(inputFile);
    }

    if (!bam.isBinary()) {
      throw new SAMException("Input file must be bam file, not sam file.");
    }

    if (!bam.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.coordinate)) {
      throw new SAMException("Input bam file must be sorted by coordinates");
    }

    BAMIndexer.createIndex(bam, OUTPUT);

    log.info("Successfully wrote bam index file " + OUTPUT);
    CloserUtil.close(bam);
    return 0;
  }