Class SamFiles


  • public class SamFiles
    extends Object
    • 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.