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

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

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    Mockito.when(datasetList.execute()).thenReturn(new ListDatasetsResponse()
        .setDatasets(Lists.newArrayList(
            new Dataset().setId("id1").setName("name").setProjectNumber(1234L))));

    // Readset summary
    Mockito.when(readsets.search(new SearchReadGroupSetsRequest()
        .setDatasetIds(Lists.newArrayList("id1")).setPageSize(100)))
        .thenReturn(readsetSearch);
    Mockito.when(readsetSearch.execute()).thenReturn(new SearchReadGroupSetsResponse()
        .setReadGroupSets(Lists.newArrayList(new ReadGroupSet(), new ReadGroupSet())));
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    command.name = "12878";

    Mockito.when(datasets.get("dataset")).thenReturn(datasetGet);
    Mockito.when(datasetGet.execute()).thenReturn(new Dataset().setId("id").setName("1kg"));

    Mockito.when(readsets.search(new SearchReadGroupSetsRequest()
        .setDatasetIds(Lists.newArrayList("dataset"))
        .setName("12878")
        .setPageSize(10)))
        .thenReturn(readsetSearch);
    Mockito.when(readsetSearch.execute()).thenReturn(new SearchReadGroupSetsResponse()
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    System.out.println();
  }

  private String getReadsetCount(Genomics genomics, String datasetId) throws IOException {
    SearchReadGroupSetsRequest readsetSearch = new SearchReadGroupSetsRequest()
        .setDatasetIds(com.google.common.collect.Lists.newArrayList(datasetId))
        .setPageSize(100);

    SearchReadGroupSetsResponse readGroupSets = genomics.readgroupsets()
        .search(readsetSearch).setFields("nextPageToken,readGroupSets(id)").execute();
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    if (dataset == null) {
      return;
    }
    System.out.println("Getting read group sets from: " + dataset.getName());

    SearchReadGroupSetsRequest request = new SearchReadGroupSetsRequest()
        .setDatasetIds(Lists.newArrayList(datasetId))
        .setName(name)
        .setPageSize(getMaxResults());
    printResults(Paginator.ReadGroupSets.create(genomics), request);
  }
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Related Classes of com.google.api.services.genomics.model.SearchReadGroupSetsRequest

  • com.google.cloud.genomics.api.client.commands.BaseCommand
  • com.google.cloud.genomics.api.client.commands.ListDatasetsCommandTest
  • com.google.cloud.genomics.api.client.commands.SearchReadGroupSetsCommand
  • com.google.cloud.genomics.api.client.commands.SearchReadGroupSetsCommandTest
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