Package abra

Examples of abra.RegionLoader.load()

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  public void run(String input, String regionsGtf) throws IOException {
   
    SAMFileReader reader = new SAMFileReader(new File(input));
   
    RegionLoader loader = new RegionLoader();
    List<Feature> regions = loader.load(regionsGtf);
   
    regions = ReAligner.splitRegions(regions);

    for (Feature region : regions) {
     
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public class MapqEval {

  public void eval(String input, String bed) throws IOException {
    RegionLoader loader = new RegionLoader();
    List<Feature> regions = loader.load(bed);

    int[] thresholds = new int[] { 0, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 255 };
   
   
    for (Feature region : regions) {
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