Class CountReadsOnMarkers


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

      • CountReadsOnMarkers

        public CountReadsOnMarkers​(SnpEffectPredictor snpEffectPredictor)
    • Method Detail

      • addFile

        public void addFile​(java.lang.String samFileName)
        Add a SAM/BAM file to be processed
        Parameters:
        samFileName -
      • addMarkerType

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

        public void count()
        Count markers from all files
      • getReadLengthAvg

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

        public java.lang.String html()
        Show charts in html
        Returns:
      • probabilityTable

        public java.lang.String probabilityTable​(CountByType prob)
        Show probabilities
        Parameters:
        prob - : Probabilities for each
        Returns:
        A string showing a tab delimited table
      • setVerbose

        public void setVerbose​(boolean verbose)
      • toString

        public java.lang.String toString()
        Print table to STDOUT
        Overrides:
        toString in class java.lang.Object