Class PlinkMap

java.lang.Object
org.snpeff.ped.PlinkMap

public class PlinkMap extends Object
PLINK MAP file References: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
Author:
pcingola
  • Field Details

    • debug

      public static boolean debug
  • Constructor Details

    • PlinkMap

      public PlinkMap()
    • PlinkMap

      public PlinkMap(String mapFileName)
  • Method Details

    • getChrName

      public String getChrName(int idx)
    • getGenotypeNames

      public Collection<String> getGenotypeNames()
    • getGenotypeNames

      public Integer getGenotypeNames(String idStr)
    • getId

      public String getId(int idx)
    • getPosition

      public int getPosition(int idx)
    • read

      protected void read(String mapFileName)
      Reads MAP file MAP file format (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) Space separated or tab columns: chromosome (1-22, X, Y or 0 if unplaced) rs# or snp identifier Genetic distance (morgans) Base-pair position (bp units)
      Parameters:
      dataFileName -
    • size

      public int size()