Class CountReadsOnMarkers

java.lang.Object
org.snpeff.coverage.CountReadsOnMarkers

public class CountReadsOnMarkers extends Object
Count how many reads map (from many SAM/BAM files) onto markers
Author:
pcingola
  • Field Details

  • Constructor Details

  • Method Details

    • addFile

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

      public void addMarkerType(Marker marker, String type)
    • count

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

      public MarkerTypes getMarkerTypes()
    • getReadLengthAvg

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

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

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