Package org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading

Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.HaplotypeGraph

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        // Determine the kmerSize to use for the unified haplotype assembly graph

        kmerSize = Math.min(minHaplotypeLength,
                heterogeneousKmerSizeResolution.useMaximum() ? assemblyResultSet.getMaximumKmerSize() : assemblyResultSet.getMinimumKmerSize());

        haplotypeGraph = new HaplotypeGraph(kmerSize,haplotypes);


        if (haplotypeGraph.hasCycles())
            Utils.warnUser(logger, "cycle caused at merging haplotypes with different kmerSizes: active region " + assemblyResultSet.getRegionForGenotyping() + " will be skipped");
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*/
public class HaplotypeGraphUnitTest extends BaseTest {

   @Test(dataProvider="buildByStringDataProvider")
   public void testBuildByString(final String string, final int kmerSize, final int vertexCount, final int edgeCount) {
       final HaplotypeGraph g = new HaplotypeGraph(string);
       Assert.assertEquals(g.getKmerSize(),kmerSize,g.toString());
       Assert.assertEquals(g.vertexSet().size(),vertexCount,g.toString());
       Assert.assertEquals(g.edgeSet().size(),edgeCount,g.toString());
   }
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   @DataProvider(name="mergingCommonChainsDataProvider")
   public Iterator<Object[]> mergingCommonChainsDataProvider() {
      final List<Object[]> list = new LinkedList<>();
      for (int i = 0; i < MERGING_COMMON_CHAINS_DATA.length; i += 2) {
          final HaplotypeGraph before = new HaplotypeGraph(MERGING_COMMON_CHAINS_DATA[i]);
          final HaplotypeGraph after = new HaplotypeGraph(MERGING_COMMON_CHAINS_DATA[i+1]);
          list.add(new Object[] { before , after});
      }
      return list.iterator();
   }
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   @DataProvider(name="equalTestDataProvider")
   public Iterator<Object[]> equalsTestDataProvider() {
      final List<Object[]> result = new LinkedList<>();
      for (int i = 0; i < EQUAL_TEST_DATA.length; i += 3) {
          final HaplotypeGraph g1 = new HaplotypeGraph(EQUAL_TEST_DATA[i]);
          final HaplotypeGraph g2 = new HaplotypeGraph(EQUAL_TEST_DATA[i+1]);
          final boolean outcome = Boolean.parseBoolean(EQUAL_TEST_DATA[i+2]);
          result.add(new Object[] { g1, g2, outcome});
      }
      return result.iterator();
   }
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Related Classes of org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.HaplotypeGraph

  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.GraphBasedLikelihoodCalculationEngineInstance
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.graphs.HaplotypeGraphUnitTest
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeRoute
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.Kmer
  • org.broadinstitute.gatk.utils.collections.CountSet
  • org.broadinstitute.gatk.utils.haplotype.Haplotype
  • java.io.File
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