Examples of ReadGroupSet

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

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    // 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())));

    // Variant set
    Mockito.when(variantSets.get("id1")).thenReturn(variantSetGet);
    Mockito.when(variantSetGet.execute()).thenReturn(new VariantSet().setReferenceBounds(
        Lists.newArrayList(new ReferenceBound().setReferenceName("contigX"))));
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Examples of com.google.api.services.genomics.model.ReadGroupSet

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    command.readGroupSetIds = Lists.newArrayList("r1", "r2");

    Mockito.when(readsets.get("r1")).thenReturn(readsetGet);
    Mockito.when(readsets.get("r2")).thenReturn(readsetGet);
    Mockito.when(readsetGet.execute()).thenReturn(
        new ReadGroupSet().setName("name1"),
        new ReadGroupSet().setName("name2"));

    command.handleRequest(genomics);

    String output = outContent.toString();
    assertTrue(output, output.contains("name1"));
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Examples of com.google.api.services.genomics.model.ReadGroupSet

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    // Get the readsets
    Mockito.when(readsets.get("r1")).thenReturn(readsetGet);
    Mockito.when(readsets.get("r2")).thenReturn(readsetGet);
    Mockito.when(readsetGet.execute()).thenReturn(
        new ReadGroupSet().setName("name1"),
        new ReadGroupSet().setName("name2"));

    // Export them
    Mockito.when(readsets.export(Mockito.any(ExportReadGroupSetsRequest.class)))
        .thenReturn(readsetExport);
    Mockito.when(readsetExport.execute()).thenReturn(
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Examples of com.google.api.services.genomics.model.ReadGroupSet

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    printJob(job);

    // If the job is finished, get the imported ids
    if (job.getImportedIds() != null) {
      for (String id : job.getImportedIds()) {
        ReadGroupSet readGroupSet = genomics.readgroupsets().get(id)
            .setFields("id,name,filename").execute();
        System.out.println("Imported read group set: " + readGroupSet.toPrettyString());
      }
    }
  }
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