Package org.snpeff.stats

Class GeneCountByTypeTable

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Iterable<java.lang.String>
    public class GeneCountByTypeTable
extends java.lang.Object
implements java.lang.Iterable<java.lang.String>, java.io.Serializable
    Count for each 'type' and 'gene'. Tries to avoid multiple counting by comparing to latest variants. WARNING: This strategy does not work if changeEffect are out of order.
    Author:
    pcingola
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static boolean debug  
      static int GENE_CPG_NUM_BINS  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.lang.String getBioType​(java.lang.String key)  
      CountByType getCounter​(java.lang.String type)
      Get counter for this type
      CountByType getCounterSize​(java.lang.String type)
      Get size counter for this type
      java.util.List<java.lang.String> getKeyList()
      Get a sorted list of keys
      int getSizeByType​(java.lang.String key, java.lang.String type)  
      java.util.List<java.lang.String> getTypeList()
      Get a sorted list of keys
      java.util.Iterator<java.lang.String> iterator()  
      void sample​(Gene gene, Transcript tr, java.lang.String type, VariantEffect variantEffect)
      Sample this tuple to update statistics

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

      • Methods inherited from interface java.lang.Iterable

        forEach, spliterator

    • Field Detail

      • GENE_CPG_NUM_BINS

        public static int GENE_CPG_NUM_BINS

      • debug

        public static boolean debug

    • Constructor Detail

      • GeneCountByTypeTable

        public GeneCountByTypeTable()

    • Method Detail

      • getBioType

        public java.lang.String getBioType​(java.lang.String key)

      • getCounter

        public CountByType getCounter​(java.lang.String type)
        Get counter for this type

      • getCounterSize

        public CountByType getCounterSize​(java.lang.String type)
        Get size counter for this type

      • getKeyList

        public java.util.List<java.lang.String> getKeyList()
        Get a sorted list of keys

      • getSizeByType

        public int getSizeByType​(java.lang.String key,
                         java.lang.String type)

      • getTypeList

        public java.util.List<java.lang.String> getTypeList()
        Get a sorted list of keys

      • iterator

        public java.util.Iterator<java.lang.String> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<java.lang.String>

      • sample

        public void sample​(Gene gene,
                   Transcript tr,
                   java.lang.String type,
                   VariantEffect variantEffect)
        Sample this tuple to update statistics