Package org.snpeff

Class RegulationFileConsensus


  • public class RegulationFileConsensus
    extends java.lang.Object
    Create a regulation consensus from a regulation file.
    Author:
    pcingola
    • Constructor Detail

      • RegulationFileConsensus

        public RegulationFileConsensus()
    • Method Detail

      • consensus

        public void consensus​(Regulation reg)
        Add to consensus
      • getRegTypes

        public java.util.Collection<java.lang.String> getRegTypes()
      • getRegulationList

        public java.util.ArrayList<Regulation> getRegulationList​(java.lang.String regType)
        Get regulation list by type (or create a new list)
      • readFile

        public void readFile​(RegulationFileIterator regulationFileIterator)
        Read a file and add all regulation intervals
      • save

        public void save()
        Save databases (one file per regType)
      • setOutputDir

        public void setOutputDir​(java.lang.String outputDir)
      • setVerbose

        public void setVerbose​(boolean verbose)