Package abra

Examples of abra.CompareToReference2

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  private CompareToReference2 c2r;
  private int minBaseQual;

  public void call(String normal, String tumor, String vcf, String reference, int minBaseQual) throws IOException {
    loadLoci(vcf);
    c2r = new CompareToReference2();
    c2r.init(reference);
    this.minBaseQual = minBaseQual;
   
    System.err.println("Processing positions");
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  private CompareToReference2 c2r;
  private Map<Integer, Long> qualityCounts;
  private Map<Integer, Long> qualityMismatches;

  public void run(String input, String ref) throws IOException {
    c2r = new CompareToReference2();
    c2r.init(ref);
   
    qualityMismatches = new HashMap<Integer, Long>();
    qualityCounts = new HashMap<Integer, Long>();
   
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  private ReadLocusReader normal;
  private ReadLocusReader tumor;
  private CompareToReference2 c2r;

  public void callSomatic(String reference, String normal, String tumor) throws IOException {
    c2r = new CompareToReference2();
    c2r.init(reference);
   
    this.normal = new ReadLocusReader(normal);
    this.tumor = new ReadLocusReader(tumor);
   
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    this.minAltFraction = minAltFraction;
    this.minAltObs = minAltObs;
    this.minMapq = minMapq;
    this.minDistanceFromIndel = minDistanceFromIndel;
   
    c2r = new CompareToReference2();
    c2r.init(reference);
   
    outputHeader();
   
    this.sample = new ReadLocusReader(bam);
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Related Classes of abra.CompareToReference2

  • abra.cadabra.Cadabra
  • abra.cadabra.SimpleCaller
  • abra.cadabra.SomaticLocusCaller
  • abra.utils.MismatchBaseQuality
  • java.io.BufferedReader
  • java.io.FileReader
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