Class CountReadsOnMarkers

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