Examples of AlignReadGroupSetsRequest

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

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

    // Import them
    Mockito.when(readsets.align(new AlignReadGroupSetsRequest()
        .setDatasetId("abc").setBamSourceUris(Lists.newArrayList("uri1"))))
        .thenReturn(readsetAlign);
    Mockito.when(readsetAlign.execute()).thenReturn(
        new AlignReadGroupSetsResponse().setJobId("8675309"));
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Examples of com.google.api.services.genomics.model.AlignReadGroupSetsRequest

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      required = true)
  public List<String> fastqFiles;

  @Override
  protected AlignReadGroupSetsRequest getRequest() {
    return new AlignReadGroupSetsRequest()
        .setInterleavedFastqSource(new InterleavedFastqSource()
            .setSourceUris(fastqFiles)
            .setMetadata(getMetadata()));
  }
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Examples of com.google.api.services.genomics.model.AlignReadGroupSetsRequest

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      required = true)
  public List<String> secondFastqFiles;

  @Override
  protected AlignReadGroupSetsRequest getRequest() {
    return new AlignReadGroupSetsRequest()
        .setPairedFastqSource(new PairedFastqSource()
            .setFirstSourceUris(firstFastqFiles)
            .setSecondSourceUris(secondFastqFiles)
            .setMetadata(getMetadata()));
  }
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Examples of com.google.api.services.genomics.model.AlignReadGroupSetsRequest

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      required = true)
  public List<String> bamFiles;

  @Override
  protected AlignReadGroupSetsRequest getRequest() {
    return new AlignReadGroupSetsRequest().setBamSourceUris(bamFiles);
  }
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