Class BamIndexValidator

java.lang.Object
htsjdk.samtools.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 Details

    • BamIndexValidator

      public BamIndexValidator()
  • Method Details

    • 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