Class CountReads


  • public class CountReads
    extends java.lang.Object
    Count how many reads map (from many SAM/BAM files) onto markers
    Author:
    pcingola
    • Field Detail

      • SHOW_EVERY

        public static int SHOW_EVERY
    • Constructor Detail

      • CountReads

        public CountReads​(java.lang.String fileName,
                          SnpEffectPredictor snpEffectPredictor)
    • Method Detail

      • addMarkerType

        public void addMarkerType​(Marker marker,
                                  java.lang.String type)
      • count

        public void count()
        Count markers from a file
      • getCountExceptions

        public int getCountExceptions()
      • getCountTotalReads

        public int getCountTotalReads()
      • getCoverageByExons

        public java.util.ArrayList<CoverageByType> getCoverageByExons()
      • getReadLengthAvg

        public int getReadLengthAvg()
        Average read length
        Returns:
      • getReadLengthCount

        public int getReadLengthCount()
      • getReadLengthSum

        public long getReadLengthSum()
      • setMarkerTypes

        public void setMarkerTypes​(MarkerTypes markerTypes)
      • setVerbose

        public void setVerbose​(boolean verbose)