Пример #1
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  /**
   * Generates a BAM index file, either textual or binary, from an input BAI file. Only used for
   * testing, but located here for visibility into CachingBAMFileIndex.
   *
   * @param output BAM Index (.bai) file (or bai.txt file when text)
   * @param textOutput Whether to create text output or binary
   */
  public static void createAndWriteIndex(
      final File input, final File output, final boolean textOutput) {

    // content is from an existing bai file.

    final CachingBAMFileIndex existingIndex = new CachingBAMFileIndex(input, null);
    final int n_ref = existingIndex.getNumberOfReferences();
    final BAMIndexWriter outputWriter;
    if (textOutput) {
      outputWriter = new TextualBAMIndexWriter(n_ref, output);
    } else {
      outputWriter = new BinaryBAMIndexWriter(n_ref, output);
    }

    // write the content one reference at a time
    try {
      for (int i = 0; i < n_ref; i++) {
        outputWriter.writeReference(existingIndex.getQueryResults(i));
      }
      outputWriter.writeNoCoordinateRecordCount(existingIndex.getNoCoordinateCount());
      outputWriter.close();

    } catch (final Exception e) {
      throw new SAMException("Exception creating BAM index", e);
    }
  }
Пример #2
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 /** write out any references between the currentReference and the nextReference */
 private void advanceToReference(final int nextReference) {
   while (currentReference < nextReference) {
     final BAMIndexContent content = indexBuilder.processReference(currentReference);
     outputWriter.writeReference(content);
     currentReference++;
     if (currentReference < numReferences) {
       indexBuilder.startNewReference();
     }
   }
 }
Пример #3
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 /**
  * After all the alignment records have been processed, finish is called. Writes any final
  * information and closes the output file.
  */
 public void finish() {
   // process any remaining references
   advanceToReference(numReferences);
   outputWriter.writeNoCoordinateRecordCount(indexBuilder.getNoCoordinateRecordCount());
   outputWriter.close();
 }