Package org.broad.igv.sam

Examples of org.broad.igv.sam.AlignmentDataManager$DownsampleOptions

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     * @param end
     * @return
     */
    private AlignmentBlock[] getBlocks(AlignmentTrack alTrack, String chr, int start, int end) {

        AlignmentDataManager dataManager = alTrack.getDataManager();
        AlignmentInterval interval = dataManager.getLoadedInterval(FrameManager.getDefaultFrame().getCurrentRange());
        if (interval == null) {
            dataManager.loadAlignments(chr, start, end, null, null);
            interval = dataManager.getLoadedInterval(FrameManager.getDefaultFrame().getCurrentRange());
        }

        return interval.getAlignmentIterator().next().getAlignmentBlocks();

    }
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     */
    private List<Object> basicRunCufflinks(String chr, int start, int end, File inFile) throws Exception{

        //Load some alignment data
        ResourceLocator locator = new ResourceLocator(inFile.getAbsolutePath());
        AlignmentDataManager dataManager = new AlignmentDataManager(locator, genome);
        AlignmentTrack alignmentTrack = new AlignmentTrack(locator, dataManager, genome);
        dataManager.loadAlignments(chr, start, end, null, null);

        PluginSpecReader.Command command = tool.commandList.get(0);

        List<Argument> argumentList = command.argumentList;

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        if(alignmentTrack == null) return -1;


        File outFile = new File(outPath);
        try {
            AlignmentDataManager dataManager = alignmentTrack.getDataManager();
            ResourceLocator inlocator = dataManager.getLocator();
            Range range = frame.getCurrentRange();

            //Read directly from file
            //return SAMWriter.writeAlignmentFilePicard(inlocator, outPath, range.getChr(), range.getStart(), range.getEnd());
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Related Classes of org.broad.igv.sam.AlignmentDataManager$DownsampleOptions

  • org.broad.igv.cli_plugin.CufflinksPluginTest
  • org.broad.igv.feature.Range
  • org.broad.igv.PreferenceManager
  • org.broad.igv.track.TrackMenuUtils
  • org.broad.igv.ui.event.DataLoadedEvent
  • org.broad.igv.ui.PreferencesEditorTest
  • org.broad.igv.ui.util.ProgressMonitor
  • org.broad.igv.util.NamedRunnable
  • java.awt.event.ActionListener
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