org.broad.tools
Class TDFTools

java.lang.Object
  org.broad.tools.TDFTools

public class TDFTools
extends java.lang.Object

Class to create TDF files from BAM files.

Author:

jrobinso, Thomas Abeel

Constructor Summary

TDFTools()

Method Summary

void	doCount(java.lang.String ifile, java.lang.String ofile, java.util.Collection<WindowFunction> windowFunctions) Compute coverage or density of an alignment or feature file.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TDFTools

public TDFTools()

Method Detail

doCount

public void doCount(java.lang.String ifile,
                    java.lang.String ofile,
                    java.util.Collection<WindowFunction> windowFunctions)
             throws java.io.IOException,
                    java.net.URISyntaxException

Compute coverage or density of an alignment or feature file.

Parameters:

ifile - BAM Alignment

ofile - Output file

windowFunctions -

windowSizeValue -

extFactorValue -

strandOption -

Throws:

java.io.IOException

java.net.URISyntaxException

ReadFailedException