Class MarkerUtil


  • public class MarkerUtil
    extends java.lang.Object
    Generic utility methods for Markers
    Author:
    pcingola
    • Constructor Summary

      Constructors 
      Constructor Description
      MarkerUtil()  
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static java.util.Map<Marker,​Marker> collapseZeroGap​(Markers markersOri)
      Collapse adjacent intervals (i.e.
      static Markers readTxt​(java.lang.String fileName, Genome genome, int positionBase)
      Read intervals from a file using a simplt TXT format Format: chr \t start \t end \t id Note: Zero-based positions
      static java.util.Map<Marker,​Marker> redundant​(java.util.Collection<? extends Marker> markersOri)
      Redundant markers in a list: Find intervals that are totally included in other intervals in the list
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • MarkerUtil

        public MarkerUtil()
    • Method Detail

      • collapseZeroGap

        public static java.util.Map<Marker,​Marker> collapseZeroGap​(Markers markersOri)
        Collapse adjacent intervals (i.e. intervals separated by a gap of zero length E.g.: The markers [1-100] and [101-200] are collapsed into one single marker [1-200]
        Returns:
        A set of new markers that can replace the old ones, or the same set if no change is required.
      • readTxt

        public static Markers readTxt​(java.lang.String fileName,
                                      Genome genome,
                                      int positionBase)
        Read intervals from a file using a simplt TXT format Format: chr \t start \t end \t id Note: Zero-based positions
        Parameters:
        fileName - : Path to file
        genome - : Genome to use. Can be null (a new one will be created)
        positionBase - : Position offset. Use '1' for one-based coordinates and '0' for zero-based coordinates.
      • redundant

        public static java.util.Map<Marker,​Marker> redundant​(java.util.Collection<? extends Marker> markersOri)
        Redundant markers in a list: Find intervals that are totally included in other intervals in the list
        Parameters:
        markersOri -
        Returns:
        A map markerIncluded -> markerLarge, where markerIncluded in completely included in markerLarge WARNING: Markers having start > end (i.e. circular chromosome with uncorrected coordinates) are not processed correctly by this method (they are explicitly ignored)