standalone


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    Description of how Standalone AutoCSA can be integrated into a pipeline.
    <br/><br/>
    If you wish to use this package as part of your pipeline, but with more control of the processing, the following methods do the actual work and must be run in the following order:
    <br/>

    <ul>
      <li>Populate a TraceGroupBean via {@link uk.ac.sanger.cgp.standalonecsa.interfaces.FileLocatorService#getAmplimerGroup(List files, AmplimerBean amplimer)}, or by constructing in a way suitable for your system.</li>
      <li>
        Call {@link uk.ac.sanger.cgp.standalonecsa.interfaces.AnalysisService#analyseTraceGroup(TraceGroupBean tgb)}
      </li>
      <li>
        Call {@link uk.ac.sanger.cgp.standalonecsa.interfaces.AnalysisService#compareTraceGroup(TraceGroupBean tgb)}
      </li>
    </ul>

    <ul>
      <b>AnalysisService.analyseTraceGroup(TraceGroupBean tgb)</b> performs:
      <ul>
        <li>initial trace analysis</li>
      </ul>
      <b>AnalysisService.compareTraceGroup(TraceGroupBean tgb)</b> performs:
      <ul>
        <li>comparison of sample and reference</li>
        <li>flagging (based on sandaloneCsa.properties)</li>
        <li>annotation</li>
        <li>removal of variants outside of ROI (based on sandaloneCsa.properties)</li>
      </ul>
    </ul>

    This will give you the raw results from the analysis system.

    <ul>
      If you wish to generate images:
      <ul>
        <li>To generate a full trace image call:<br/><b>{@link uk.ac.sanger.cgp.standalonecsa.interfaces.ChromatogramService#generateFullChrom(String imageLoc, ExperimentBean expBean, boolean writeImage, boolean drawBaseChar)}</b></li>
        <li>To generate the 4 images as used in the variant view call:<br/><b>{@link uk.ac.sanger.cgp.standalonecsa.interfaces.ChromatogramService#generateVariantViewSet(String imageLoc, ExperimentBean expBean, ExperimentBean normExp, boolean drawBaseChar, boolean writeToFile)}</b></li>
        <li>As previous, but only generates the image for the specified ExperimentBean call:<br/><b>{@link uk.ac.sanger.cgp.standalonecsa.interfaces.ChromatogramService#generateVariantViewSingle(String pathRoot, ExperimentBean expBean, boolean writeToFile, boolean drawBaseChar)}</b></li>
        <li>To generate the image as used in the complex variant view call:<br/><b>{@link uk.ac.sanger.cgp.standalonecsa.interfaces.ChromatogramService#generateComplexVariantView(String pathRoot, ExperimentBean expBean, ExperimentBean wtExp, boolean drawBaseChar, boolean writeToFile)}</b></li>
      </ul>
    </ul>
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