Constructor Detail

• SamFiles

  public SamFiles()

Method Detail

• findIndex

  public static File findIndex​(File samFile)

  Finds the index file associated with the provided SAM file. The index file must exist and be reachable to be found. If the file is a symlink and the index cannot be found, try to unsymlink the file and look for the bai in the actual file path.

  Returns:

  The index for the provided SAM, or null if one was not found.

• findIndex

  public static Path findIndex​(Path samPath)

  Finds the index file associated with the provided SAM file. The index file must exist and be reachable to be found. If the file is a symlink and the index cannot be found, try to unsymlink the file and look for the bai in the actual file path.

  Returns:

  The index for the provided SAM, or null if one was not found.