Ejemplo n.º 1
0
  // necessary to not overload equals for genotypes
  private void assertGenotypesAreMostlyEqual(GenotypesContext actual, GenotypesContext expected) {
    if (actual == expected) {
      return;
    }

    if (actual == null || expected == null) {
      Assert.fail("Maps not equal: expected: " + expected + " and actual: " + actual);
    }

    if (actual.size() != expected.size()) {
      Assert.fail("Maps do not have the same size:" + actual.size() + " != " + expected.size());
    }

    for (Genotype value : actual) {
      Genotype expectedValue = expected.get(value.getSampleName());

      Assert.assertEquals(
          value.getAlleles(), expectedValue.getAlleles(), "Alleles in Genotype aren't equal");
      Assert.assertEquals(value.getGQ(), expectedValue.getGQ(), "GQ values aren't equal");
      Assert.assertEquals(
          value.hasLikelihoods(),
          expectedValue.hasLikelihoods(),
          "Either both have likelihoods or both not");
      if (value.hasLikelihoods())
        Assert.assertEquals(
            value.getLikelihoods().getAsVector(),
            expectedValue.getLikelihoods().getAsVector(),
            "Genotype likelihoods aren't equal");
    }
  }
  public static GenotypesContext stripPLs(GenotypesContext genotypes) {
    GenotypesContext newGs = GenotypesContext.create(genotypes.size());

    for (final Genotype g : genotypes) {
      newGs.add(g.hasLikelihoods() ? removePLs(g) : g);
    }

    return newGs;
  }
Ejemplo n.º 3
0
 /** @return the number of samples in the context */
 public int getNSamples() {
   return genotypes.size();
 }