Class TargetMetricsCollector.Coverage

    • Field Summary

      Fields 
      Modifier and Type Field Description
      long readCount  
    • 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.
    • Field Detail

      • readCount

        public long readCount
    • Constructor Detail

      • 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 Detail

      • 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()