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.