Class BamIndexValidator


  • public class BamIndexValidator
    extends Object
    Class to validate (at two different levels of thoroughness) the index for a BAM file. This class is [not] thread safe [because it is immutable].
    • Constructor Detail

      • BamIndexValidator

        public BamIndexValidator()
    • Method Detail

      • exhaustivelyTestIndex

        public static int exhaustivelyTestIndex​(SamReader reader)
      • lessExhaustivelyTestIndex

        public static int lessExhaustivelyTestIndex​(SamReader reader)
        A less time-consuming index validation that only looks at the first and last references in the index and the first and last chunks in each of those
        Parameters:
        reader -
        Returns:
        # of chunks examined, or 0 if there is no browseable index for the reader