Class TargetMetricsCollector.Coverage

java.lang.Object
picard.analysis.directed.TargetMetricsCollector.Coverage
Enclosing class:
TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics>

public static class TargetMetricsCollector.Coverage extends Object
A simple class that is used to store the coverage information about an interval.
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    long
     
  • Constructor Summary

    Constructors
    Constructor
    Description
    Coverage(htsjdk.samtools.util.Interval i, int padding)
    Constructs a new coverage object for the provided mapping with the desired padding either side.
  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addBase(int offset)
    Adds a single point of depth at the desired offset into the coverage array.
    void
    addBase(int offset, int depth)
    Adds some depth at the desired offset into the coverage array.
    int[]
    Gets the coverage depths as an array of ints.
    long
     
    boolean
    Returns true if any base in the range has coverage of > 0
    void
    Increments the # of reads mapping to this target.
     

    Methods inherited from class java.lang.Object

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

    • readCount

      public long readCount
  • Constructor Details

    • Coverage

      public Coverage(htsjdk.samtools.util.Interval i, int padding)
      Constructs a new coverage object for the provided mapping with the desired padding either side.
  • Method Details

    • addBase

      public void addBase(int offset)
      Adds a single point of depth at the desired offset into the coverage array.
    • addBase

      public void addBase(int offset, int depth)
      Adds some depth at the desired offset into the coverage array.
    • incrementReadCount

      public void incrementReadCount()
      Increments the # of reads mapping to this target.
    • hasCoverage

      public boolean hasCoverage()
      Returns true if any base in the range has coverage of > 0
    • getDepths

      public int[] getDepths()
      Gets the coverage depths as an array of ints.
    • getTotal

      public long getTotal()
    • toString

      public String toString()
      Overrides:
      toString in class Object