Package picard.analysis

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
    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.

  • Constructor Summary

    Constructors
    Constructor
    Description
    JumpingLibraryMetrics()
     

  • 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()