Package org.broad.igv.sam

Examples of org.broad.igv.sam.AlignmentInterval$AlignmentIterator


     * @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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