Class JumpingLibraryMetrics


  • @DocumentedFeature(groupName="Metrics",
                       summary="Metrics")
    public class JumpingLibraryMetrics
    extends htsjdk.samtools.metrics.MetricBase
    High level metrics about the presence of outward- and inward-facing pairs within a SAM file generated with a jumping library, produced by the CollectJumpingLibraryMetrics program and usually stored in a file with the extension ".jump_metrics".
    • Field Summary

      Fields 
      Modifier and Type Field Description
      long CHIMERIC_PAIRS
      The number of pairs where either (a) the ends fall on different chromosomes or (b) the insert size is greater than the maximum of 100000 or 2 times the mode of the insert size for outward-facing pairs.
      long FRAGMENTS
      The number of fragments in the SAM file
      long JUMP_DUPLICATE_PAIRS
      The number of outward-facing pairs that are duplicates
      double JUMP_DUPLICATE_PCT
      The fraction of outward-facing pairs that are marked as duplicates
      long JUMP_LIBRARY_SIZE
      The estimated library size for outward-facing pairs
      double JUMP_MEAN_INSERT_SIZE
      The mean insert size for outward-facing pairs
      long JUMP_PAIRS
      The number of outward-facing pairs in the SAM file
      double JUMP_STDEV_INSERT_SIZE
      The standard deviation on the insert size for outward-facing pairs
      long NONJUMP_DUPLICATE_PAIRS
      The number of inward-facing pais that are duplicates
      double NONJUMP_DUPLICATE_PCT
      The fraction of inward-facing pairs that are marked as duplicates
      long NONJUMP_LIBRARY_SIZE
      The estimated library size for inward-facing pairs
      double NONJUMP_MEAN_INSERT_SIZE
      The mean insert size for inward-facing pairs
      long NONJUMP_PAIRS
      The number of inward-facing pairs in the SAM file
      double NONJUMP_STDEV_INSERT_SIZE
      The standard deviation on the insert size for inward-facing pairs
      double PCT_CHIMERAS
      The number of chimeric pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
      double PCT_JUMPS
      The number of outward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
      double PCT_NONJUMPS
      The number of inward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
    • Field Detail

      • JUMP_PAIRS

        public long JUMP_PAIRS
        The number of outward-facing pairs in the SAM file
      • JUMP_DUPLICATE_PAIRS

        public long JUMP_DUPLICATE_PAIRS
        The number of outward-facing pairs that are duplicates
      • JUMP_DUPLICATE_PCT

        public double JUMP_DUPLICATE_PCT
        The fraction of outward-facing pairs that are marked as duplicates
      • JUMP_LIBRARY_SIZE

        public long JUMP_LIBRARY_SIZE
        The estimated library size for outward-facing pairs
      • JUMP_MEAN_INSERT_SIZE

        public double JUMP_MEAN_INSERT_SIZE
        The mean insert size for outward-facing pairs
      • JUMP_STDEV_INSERT_SIZE

        public double JUMP_STDEV_INSERT_SIZE
        The standard deviation on the insert size for outward-facing pairs
      • NONJUMP_PAIRS

        public long NONJUMP_PAIRS
        The number of inward-facing pairs in the SAM file
      • NONJUMP_DUPLICATE_PAIRS

        public long NONJUMP_DUPLICATE_PAIRS
        The number of inward-facing pais that are duplicates
      • NONJUMP_DUPLICATE_PCT

        public double NONJUMP_DUPLICATE_PCT
        The fraction of inward-facing pairs that are marked as duplicates
      • NONJUMP_LIBRARY_SIZE

        public long NONJUMP_LIBRARY_SIZE
        The estimated library size for inward-facing pairs
      • NONJUMP_MEAN_INSERT_SIZE

        public double NONJUMP_MEAN_INSERT_SIZE
        The mean insert size for inward-facing pairs
      • NONJUMP_STDEV_INSERT_SIZE

        public double NONJUMP_STDEV_INSERT_SIZE
        The standard deviation on the insert size for inward-facing pairs
      • CHIMERIC_PAIRS

        public long CHIMERIC_PAIRS
        The number of pairs where either (a) the ends fall on different chromosomes or (b) the insert size is greater than the maximum of 100000 or 2 times the mode of the insert size for outward-facing pairs.
      • FRAGMENTS

        public long FRAGMENTS
        The number of fragments in the SAM file
      • PCT_JUMPS

        public double PCT_JUMPS
        The number of outward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
      • PCT_NONJUMPS

        public double PCT_NONJUMPS
        The number of inward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
      • PCT_CHIMERAS

        public double PCT_CHIMERAS
        The number of chimeric pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
    • Constructor Detail

      • JumpingLibraryMetrics

        public JumpingLibraryMetrics()