Class JumpingLibraryMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.analysis.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
    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
    The number of fragments in the SAM file
    long
    The number of outward-facing pairs that are duplicates
    double
    The fraction of outward-facing pairs that are marked as duplicates
    long
    The estimated library size for outward-facing pairs
    double
    The mean insert size for outward-facing pairs
    long
    The number of outward-facing pairs in the SAM file
    double
    The standard deviation on the insert size for outward-facing pairs
    long
    The number of inward-facing pais that are duplicates
    double
    The fraction of inward-facing pairs that are marked as duplicates
    long
    The estimated library size for inward-facing pairs
    double
    The mean insert size for inward-facing pairs
    long
    The number of inward-facing pairs in the SAM file
    double
    The standard deviation on the insert size for inward-facing pairs
    double
    The number of chimeric pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
    double
    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
    The number of inward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Methods inherited from class htsjdk.samtools.metrics.MetricBase

    equals, hashCode, toString

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
  • Field Details

    • 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 Details

    • JumpingLibraryMetrics

      public JumpingLibraryMetrics()