Class CountReads

java.lang.Object
org.snpeff.coverage.CountReads

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

    • SHOW_EVERY

      public static int SHOW_EVERY
  • Constructor Details

  • Method Details

    • addMarkerType

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

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

      public CountByKey<Marker> getCountBases()
    • getCountExceptions

      public int getCountExceptions()
    • getCountReads

      public CountByKey<Marker> getCountReads()
    • getCountTotalReads

      public int getCountTotalReads()
    • getCountTypes

      public CountByType getCountTypes()
    • getCoverageByExons

      public ArrayList<CoverageByType> getCoverageByExons()
    • getCoverageByType

      public CoverageByType getCoverageByType()
    • getMarkerTypes

      public MarkerTypes getMarkerTypes()
    • 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)