Package com.google.api.services.genomics.model

Examples of com.google.api.services.genomics.model.VariantSet

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    Mockito.when(readsetSearch.execute()).thenReturn(new SearchReadGroupSetsResponse()
        .setReadGroupSets(Lists.newArrayList(new ReadGroupSet(), new ReadGroupSet())));

    // Variant set
    Mockito.when(variantSets.get("id1")).thenReturn(variantSetGet);
    Mockito.when(variantSetGet.execute()).thenReturn(new VariantSet().setReferenceBounds(
        Lists.newArrayList(new ReferenceBound().setReferenceName("contigX"))));

    command.handleRequest(genomics);

    String output = outContent.toString();
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        .thenReturn(readsetSearch);
    Mockito.when(readsetSearch.execute()).thenReturn(new SearchReadGroupSetsResponse());

    // Variant set
    Mockito.when(variantSets.get(Mockito.anyString())).thenReturn(variantSetGet);
    Mockito.when(variantSetGet.execute()).thenReturn(new VariantSet());

    command.handleRequest(genomics);

    String output = outContent.toString();
    assertTrue(output, output.contains("name1 (ID: id)"));
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    command.variantSetIds = Lists.newArrayList("v1", "v2");

    Mockito.when(variantSets.get("v1")).thenReturn(variantSetGet);
    Mockito.when(variantSets.get("v2")).thenReturn(variantSetGet);
    Mockito.when(variantSetGet.execute()).thenReturn(
        new VariantSet().setId("id1"),
        new VariantSet().setId("id2"));

    command.handleRequest(genomics);

    String output = outContent.toString();
    assertTrue(output, output.contains("id1"));
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    System.out.println(dataset.toPrettyString());
    System.out.print("Read group sets: ");
    System.out.println(getReadsetCount(genomics, id));

    // Variant set
    VariantSet variantSet = genomics.variantsets().get(id).setFields("referenceBounds").execute();
    if (variantSet != null && variantSet.getReferenceBounds() != null) {
      // Only print out a variant set if one exists
      System.out.println("Variant set: " + variantSet.toPrettyString());
    }

    System.out.println();
  }
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Related Classes of com.google.api.services.genomics.model.VariantSet

  • com.google.cloud.genomics.api.client.commands.BaseCommand
  • com.google.cloud.genomics.api.client.commands.GetVariantSetsCommandTest
  • com.google.cloud.genomics.api.client.commands.ListDatasetsCommandTest
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