title: PHPUnit HTML and Clover coverage reports differ due to codeCoverageIgnore
body: <p>I'm using PHPUnit 3.5.14 and have a suite of tests which covers 100% of my PHP application excluding certain portions with // @codeCoverageIgnore[Start|End].  The HTML coverage report shows 100% coverage.  But when I generate a Clover XML coverage report, which I'd like Jenkins to read to enforce the 100% coverage requirement, it shows all of my ignored code as not covered.</p>
  
  <p>For example, I have a controller class with 20 methods, one of which looks like this:</p>
  
  <pre><code>// @codeCoverageIgnoreStart
  /**
   * Gets an instance of Foo.  Abstracted for testing.
   *
   * @param array $options The constructor argument
   *
   * @return Foo
   */
  protected function _getFoo(array $options)
  {
      return new Foo($options);
  }
  // @codeCoverageIgnoreEnd
  </code></pre>
  
  <p>The HTML coverage report shows 20 methods covered including the one entirely ignored:</p>
  
  <p>pic: coverage report excerpt</p>
  
  <p><img src="https://i.stack.imgur.com/PeOP9.png" alt="enter image description here">
  <a href="https://i.imgur.com/VRtKR.png" rel="nofollow noreferrer">http://i.imgur.com/VRtKR.png</a></p>
  
  <p>But the Clover XML report shows 19/20 methods covered and doesn't mention _getFoo:</p>
  
  <pre><code>&lt;class name="CampaignController" namespace="global" (...)&gt;
    &lt;metrics methods="20" coveredmethods="19" conditionals="0" coveredconditionals="0" statements="532" coveredstatements="532" elements="552" coveredelements="551"/&gt;
  </code></pre>
  
  <p>...</p>
  
  <pre><code>  &lt;line num="592" type="stmt" count="1"/&gt;
    &lt;line num="593" type="stmt" count="1"/&gt;
    &lt;line num="615" type="method" name="createAction" crap="2" count="2"/&gt;
    &lt;line num="617" type="stmt" count="2"/&gt;
  </code></pre>
  
  <p>(The _getFoo lines at the top are lines 596-608.)</p>
  
  <p>The logging section of my PHPUnit configuration looks like this:</p>
  
  <pre><code>&lt;logging&gt;
      &lt;log type="coverage-html" target="../public/build/coverage" charset="UTF-8"
          yui="true" highlight="true" lowUpperBound="90" highLowerBound="100"/&gt;
      &lt;log type="coverage-clover" target="../public/build/test-coverage.xml"/&gt;
  &lt;/logging&gt;
  </code></pre>
  
  <p><strong>Is there a way to configure the Clover coverage log entry, or change my coverage ignore comments, so that the Clover report indicates 100% coverage to match the HTML report?</strong></p>