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           <string>Either a genome ID (e.g. hg18) or the full path to a .genome file.</string>
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           <string>&lt;html&gt;Specifies a &quot;bed&quot; file to be used to map probe identifiers to locations.  This option is useful &lt;br&gt;when preprocessing gct files.  The bed file should contain 4 columns: chr start end name
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         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
          <void method="setProperty">
           <string>gridx</string>
           <int>2</int>
          </void>
          <void method="setProperty">
           <string>gridy</string>
           <int>3</int>
          </void>
          <void method="setProperty">
           <string>vAlign</string>
           <int>0</int>
          </void>
          <void method="setProperty">
           <string>weightx</string>
           <double>1.0</double>
          </void>
          <void method="setProperty">
           <string>weighty</string>
           <double>1.0</double>
          </void>
         </object>
        </void>
        <void method="add">
         <object class="com.jformdesigner.model.FormComponent">
          <string>javax.swing.JButton</string>
          <void method="setProperty">
           <string>text</string>
           <string>Browse</string>
          </void>
          <void property="name">
           <string>probeButton</string>
          </void>
         </object>
         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
          <void method="setProperty">
           <string>gridx</string>
           <int>3</int>
          </void>
          <void method="setProperty">
           <string>gridy</string>
           <int>3</int>
          </void>
          <void method="setProperty">
           <string>vAlign</string>
           <int>0</int>
          </void>
          <void method="setProperty">
           <string>weighty</string>
           <double>1.0</double>
          </void>
         </object>
        </void>
        <void method="add">
         <object class="com.jformdesigner.model.FormComponent">
          <string>javax.swing.JComboBox</string>
          <void method="setProperty">
           <string>editable</string>
           <boolean>false</boolean>
          </void>
          <void method="setProperty">
           <string>model</string>
           <object class="javax.swing.DefaultComboBoxModel"/>
          </void>
          <void property="name">
           <string>zoomCombo</string>
          </void>
         </object>
         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
          <void method="setProperty">
           <string>gridx</string>
           <int>2</int>
          </void>
          <void method="setProperty">
           <string>gridy</string>
           <int>1</int>
          </void>
          <void method="setProperty">
           <string>hAlign</string>
           <int>2</int>
          </void>
          <void method="setProperty">
           <string>vAlign</string>
           <int>0</int>
          </void>
          <void method="setProperty">
           <string>weightx</string>
           <double>1.0</double>
          </void>
         </object>
        </void>
        <void method="add">
         <object class="com.jformdesigner.model.FormComponent">
          <string>javax.swing.JLabel</string>
          <void method="setProperty">
           <string>toolTipText</string>
           <string>The window size over which coverage computed when using the count command.  Defaults to 25 bp.</string>
          </void>
          <void method="setProperty">
           <string>text</string>
           <string>Window Size</string>
          </void>
          <void property="name">
           <string>windowSizeLabel</string>
          </void>
         </object>
         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
          <void method="setProperty">
           <string>gridx</string>
           <int>1</int>
          </void>
          <void method="setProperty">
           <string>gridy</string>
           <int>4</int>
          </void>
          <void method="setProperty">
           <string>hAlign</string>
           <int>2</int>
          </void>
          <void method="setProperty">
           <string>vAlign</string>
           <int>0</int>
          </void>
         </object>
        </void>
        <void method="add">
         <object class="com.jformdesigner.model.FormComponent">
          <string>javax.swing.JTextField</string>
          <void property="name">
           <string>windowSizeField</string>
          </void>
         </object>
         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
          <void method="setProperty">
           <string>gridx</string>
           <int>2</int>
          </void>
          <void method="setProperty">
           <string>gridy</string>
           <int>4</int>
          </void>
          <void method="setProperty">
           <string>vAlign</string>
           <int>0</int>
          </void>
          <void method="setProperty">
           <string>weightx</string>
           <double>1.0</double>
          </void>
         </object>
        </void>
        <void method="add">
         <object class="com.jformdesigner.model.FormComponent">
          <string>javax.swing.JLabel</string>
          <void method="setProperty">
           <string>text</string>
           <string>Extension Factor</string>
          </void>
          <void method="setProperty">
           <string>toolTipText</string>
           <string>Extend read by this amount.  Set to average fragment size of library</string>
          </void>
          <void property="name">
           <string>extFactorLabel</string>
          </void>
         </object>
         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
          <void method="setProperty">
           <string>gridx</string>
           <int>1</int>
          </void>
          <void method="setProperty">
           <string>gridy</string>
           <int>5</int>
          </void>
         </object>
        </void>
        <void method="add">
         <object class="com.jformdesigner.model.FormComponent">
          <string>javax.swing.JTextField</string>
          <void property="name">
           <string>extFactorField</string>
          </void>
         </object>
         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
          <void method="setProperty">
           <string>gridx</string>
           <int>2</int>
          </void>
          <void method="setProperty">
           <string>gridy</string>
           <int>5</int>
          </void>
         </object>
        </void>
        <void method="add">
         <object class="com.jformdesigner.model.FormComponent">
          <string>javax.swing.JCheckBox</string>
          <void method="setProperty">
           <string>text</string>
           <string>Count as Pairs</string>
          </void>
          <void method="setProperty">
           <string>toolTipText</string>
           <string>Count area between proper pairs as covered.</string>
          </void>
          <void property="name">
           <string>pairsCB</string>
          </void>
         </object>
         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
          <void method="setProperty">
           <string>gridx</string>
           <int>1</int>
          </void>
          <void method="setProperty">
           <string>gridy</string>
           <int>6</int>
          </void>
         </object>
        </void>
       </object>
       <object class="com.jformdesigner.model.FormLayoutConstraints">
        <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
        <void method="setProperty">
         <string>gridx</string>
         <int>1</int>
        </void>
        <void method="setProperty">
         <string>gridy</string>
         <int>2</int>
        </void>
        <void method="setProperty">
         <string>weightx</string>
         <double>1.0</double>
        </void>
        <void method="setProperty">
         <string>weighty</string>
         <double>1.0</double>
        </void>
       </object>
      </void>
      <void method="add">
       <object class="com.jformdesigner.model.FormContainer">
        <string>javax.swing.JPanel</string>
        <object class="com.jformdesigner.model.FormLayoutManager">
         <class>java.awt.GridBagLayout</class>
         <void method="setProperty">
          <string>$columnSpecs</string>
          <string>0, 0, 0, 0, 0</string>
         </void>
         <void method="setProperty">
          <string>$rowSpecs</string>
          <string>0, 0, 0</string>
         </void>
        </object>
        <void method="setProperty">
         <string>border</string>
         <object class="javax.swing.border.TitledBorder">
          <null/>
          <string>Sort Options</string>
          <int>4</int>
          <int>2</int>
         </object>
        </void>
        <void property="name">
         <string>sortPanel</string>
        </void>
        <void method="add">
         <object class="com.jformdesigner.model.FormComponent">
          <string>javax.swing.JLabel</string>
          <void method="setProperty">
           <string>toolTipText</string>
           <string>&lt;html&gt;Specify a temporary working directory.  For large input files this directory will be used to &lt;br&gt;store intermediate results of the sort. The default is the users temp directory.</string>
          </void>
          <void method="setProperty">
           <string>text</string>
           <string>Temp Directory</string>
          </void>
          <void property="name">
           <string>tmpDirectoryLabel</string>
          </void>
         </object>
         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
          <void method="setProperty">
           <string>gridx</string>
           <int>1</int>
          </void>
          <void method="setProperty">
           <string>gridy</string>
           <int>1</int>
          </void>
          <void method="setProperty">
           <string>hAlign</string>
           <int>2</int>
          </void>
          <void method="setProperty">
           <string>vAlign</string>
           <int>0</int>
          </void>
          <void method="setProperty">
           <string>weighty</string>
           <double>1.0</double>
          </void>
         </object>
        </void>
        <void method="add">
         <object class="com.jformdesigner.model.FormComponent">
          <string>javax.swing.JLabel</string>
          <void method="setProperty">
           <string>toolTipText</string>
           <string>&lt;html&gt;The maximum number of records to keep in memory during the sort.  The default value is &lt;br&gt;500000.  Increase this number if you receive &quot;too many open files&quot; errors.   Decrease it if you &lt;br&gt;experience &quot;out of memory&quot; errors.</string>
          </void>
          <void method="setProperty">
           <string>text</string>
           <string>Max Records</string>
          </void>
          <void property="name">
           <string>maxRecordsLabel</string>
          </void>
         </object>
         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
          <void method="setProperty">
           <string>gridx</string>
           <int>1</int>
          </void>
          <void method="setProperty">
           <string>gridy</string>
           <int>2</int>
          </void>
          <void method="setProperty">
           <string>hAlign</string>
           <int>2</int>
          </void>
          <void method="setProperty">
           <string>vAlign</string>
           <int>0</int>
          </void>
          <void method="setProperty">
           <string>weighty</string>
           <double>1.0</double>
          </void>
         </object>
        </void>
        <void method="add">
         <object class="com.jformdesigner.model.FormComponent">
          <string>javax.swing.JButton</string>
          <void method="setProperty">
           <string>text</string>
           <string>Browse</string>
          </void>
          <void property="name">
           <string>tempButton</string>
          </void>
         </object>
         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
          <void method="setProperty">
           <string>gridx</string>
           <int>4</int>
          </void>
          <void method="setProperty">
           <string>gridy</string>
           <int>1</int>
          </void>
          <void method="setProperty">
           <string>vAlign</string>
           <int>0</int>
          </void>
          <void method="setProperty">
           <string>weighty</string>
           <double>1.0</double>
          </void>
         </object>
        </void>
        <void method="add">
         <object class="com.jformdesigner.model.FormComponent">
          <string>javax.swing.JTextField</string>
          <void property="name">
           <string>tmpDirectoryField</string>
          </void>
         </object>
         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
          <void method="setProperty">
           <string>gridx</string>
           <int>3</int>
          </void>
          <void method="setProperty">
           <string>gridy</string>
           <int>1</int>
          </void>
          <void method="setProperty">
           <string>vAlign</string>
           <int>0</int>
          </void>
          <void method="setProperty">
           <string>weightx</string>
           <double>1.0</double>
          </void>
          <void method="setProperty">
           <string>weighty</string>
           <double>1.0</double>
          </void>
         </object>
        </void>
        <void method="add">
         <object class="com.jformdesigner.model.FormComponent">
          <string>javax.swing.JTextField</string>
          <void property="name">
           <string>maxRecordsField</string>
          </void>
         </object>
         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
          <void method="setProperty">
           <string>gridx</string>
           <int>3</int>
          </void>
          <void method="setProperty">
           <string>gridy</string>
           <int>2</int>
          </void>
          <void method="setProperty">
           <string>vAlign</string>
           <int>0</int>
          </void>
          <void method="setProperty">
           <string>weightx</string>
           <double>1.0</double>
          </void>
          <void method="setProperty">
           <string>weighty</string>
           <double>1.0</double>
          </void>
         </object>
        </void>
       </object>
       <object class="com.jformdesigner.model.FormLayoutConstraints">
        <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
        <void method="setProperty">
         <string>gridx</string>
         <int>1</int>
        </void>
        <void method="setProperty">
         <string>gridy</string>
         <int>3</int>
        </void>
        <void method="setProperty">
         <string>weightx</string>
         <double>1.0</double>
        </void>
        <void method="setProperty">
         <string>weighty</string>
         <double>1.0</double>
        </void>
       </object>
      </void>
      <void method="add">
       <object class="com.jformdesigner.model.FormContainer">
        <string>javax.swing.JPanel</string>
        <object class="com.jformdesigner.model.FormLayoutManager">
         <class>java.awt.GridBagLayout</class>
         <void method="setProperty">
          <string>$columnSpecs</string>
          <string>0, 0, 0</string>
         </void>
         <void method="setProperty">
          <string>$rowSpecs</string>
          <string>0</string>
         </void>
        </object>
        <void property="name">
         <string>buttonPanel</string>
        </void>
        <void method="add">
         <object class="com.jformdesigner.model.FormComponent">
          <string>javax.swing.JButton</string>
          <void method="setProperty">
           <string>text</string>
           <string>Run</string>
          </void>
          <void property="name">
           <string>runButton</string>
          </void>
         </object>
         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
          <void method="setProperty">
           <string>gridx</string>
           <int>2</int>
          </void>
          <void method="setProperty">
           <string>vAlign</string>
           <int>0</int>
          </void>
          <void method="setProperty">
           <string>weighty</string>
           <double>1.0</double>
          </void>
         </object>
        </void>
        <void method="add">
         <object class="com.jformdesigner.model.FormComponent">
          <string>javax.swing.JButton</string>
          <void method="setProperty">
           <string>text</string>
           <string>Close</string>
          </void>
          <void property="name">
           <string>closeButton</string>
          </void>
         </object>
         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
          <void method="setProperty">
           <string>gridx</string>
           <int>1</int>
          </void>
          <void method="setProperty">
           <string>vAlign</string>
           <int>0</int>
          </void>
          <void method="setProperty">
           <string>weighty</string>
           <double>1.0</double>
          </void>
         </object>
        </void>
       </object>
       <object class="com.jformdesigner.model.FormLayoutConstraints">
        <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
        <void method="setProperty">
         <string>gridx</string>
         <int>1</int>
        </void>
        <void method="setProperty">
         <string>gridy</string>
         <int>4</int>
        </void>
        <void method="setProperty">
         <string>weightx</string>
         <double>1.0</double>
        </void>
       </object>
      </void>
      <void method="add">
       <object class="com.jformdesigner.model.FormContainer">
        <string>javax.swing.JPanel</string>
        <object class="com.jformdesigner.model.FormLayoutManager">
         <class>com.jformdesigner.runtime.NullLayout</class>
        </object>
        <void method="setProperty">
         <string>border</string>
         <object class="javax.swing.border.TitledBorder">
          <object class="javax.swing.border.EmptyBorder">
           <int>0</int>
           <int>0</int>
           <int>0</int>
           <int>0</int>
          </object>
          <string>Messages</string>
          <int>4</int>
          <int>2</int>
         </object>
        </void>
        <void property="name">
         <string>OutputPanel</string>
        </void>
        <void method="add">
         <object class="com.jformdesigner.model.FormContainer">
          <string>javax.swing.JScrollPane</string>
          <object class="com.jformdesigner.model.FormLayoutManager">
           <class>javax.swing.JScrollPane</class>
          </object>
          <void property="name">
           <string>outputScroll</string>
          </void>
          <void method="add">
           <object class="com.jformdesigner.model.FormComponent">
            <string>javax.swing.JTextArea</string>
            <void method="setProperty">
             <string>editable</string>
             <boolean>false</boolean>
            </void>
            <void method="setProperty">
             <string>text</string>
             <string></string>
            </void>
            <void method="setProperty">
             <string>rows</string>
             <int>10</int>
            </void>
            <void property="name">
             <string>outputText</string>
            </void>
           </object>
          </void>
         </object>
         <object class="com.jformdesigner.model.FormLayoutConstraints">
          <class>com.jformdesigner.runtime.NullConstraints</class>
          <void method="setProperty">
           <string>x</string>
           <int>4</int>
          </void>
          <void method="setProperty">
           <string>y</string>
           <int>20</int>
          </void>
          <void method="setProperty">
           <string>width</string>
           <int>881</int>
          </void>
         </object>
        </void>
       </object>
       <object class="com.jformdesigner.model.FormLayoutConstraints">
        <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
        <void method="setProperty">
         <string>gridx</string>
         <int>1</int>
        </void>
        <void method="setProperty">
         <string>gridy</string>
         <int>6</int>
        </void>
        <void method="setProperty">
         <string>weightx</string>
         <double>1.0</double>
        </void>
       </object>
      </void>
      <void method="add">
       <object class="com.jformdesigner.model.FormComponent">
        <string>javax.swing.JSeparator</string>
        <void property="name">
         <string>separator1</string>
        </void>
        <void method="auxiliary">
         <void method="setProperty">
          <string>JavaCodeGenerator.variableLocal</string>
          <boolean>true</boolean>
         </void>
        </void>
       </object>
       <object class="com.jformdesigner.model.FormLayoutConstraints">
        <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
        <void method="setProperty">
         <string>gridx</string>
         <int>1</int>
        </void>
        <void method="setProperty">
         <string>gridy</string>
         <int>5</int>
        </void>
        <void method="setProperty">
         <string>weightx</string>
         <double>1.0</double>
        </void>
       </object>
      </void>
      <void method="add">
       <object class="com.jformdesigner.model.FormComponent">
        <string>javax.swing.JProgressBar</string>
        <void property="name">
         <string>progressBar</string>
        </void>
       </object>
       <object class="com.jformdesigner.model.FormLayoutConstraints">
        <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
        <void method="setProperty">
         <string>gridx</string>
         <int>1</int>
        </void>
        <void method="setProperty">
         <string>gridy</string>
         <int>7</int>
        </void>
        <void method="setProperty">
         <string>vAlign</string>
         <int>0</int>
        </void>
        <void method="setProperty">
         <string>weightx</string>
         <double>1.0</double>
        </void>
       </object>
      </void>
     </object>
     <object class="com.jformdesigner.model.FormLayoutConstraints">
      <null/>
      <void method="setProperty">
       <string>path</string>
       <object class="java.awt.Point">
        <int>0</int>
        <int>0</int>
       </object>
      </void>
      <void method="setProperty">
       <string>size</string>
       <object class="java.awt.Dimension">
        <int>921</int>
        <int>1347</int>
       </object>
      </void>
     </object>
    </void>
   </object>
  </void>
 </object>
</java>
