Examples with Sample com.hartwig.patient.Sample used on opensource projects

Example 11 with Sample

use of com.hartwig.patient.Sample in project pipeline5 by hartwigmedical.

the class SbpSampleReaderTest method handlesSubdirectories.

@Test
public void handlesSubdirectories() {
    returnJson(FASTQ_JSON_SUBDIRECTORIES);
    Sample sample = victim.read(EXISTS);
    assertThat(sample.lanes()).hasSize(2);
    assertThat(sample.name()).isEqualTo("CPCT02330029T");
}

Example 12 with Sample

use of com.hartwig.patient.Sample in project pipeline5 by hartwigmedical.

the class GoogleStorageSampleSourceTest method verifyFastq.

private void verifyFastq(final String firstOfPair, final String secondOfPair) {
    Bucket bucket = mock(Bucket.class);
    Blob firstBlob = TestBlobs.blob(firstOfPair);
    Blob secondBlob = TestBlobs.blob(secondOfPair);
    Page<Blob> page = TestBlobs.pageOf(firstBlob, secondBlob);
    when(bucket.list(Storage.BlobListOption.prefix("aligner/samples/"))).thenReturn(page);
    when(storage.get(Mockito.anyString())).thenReturn(bucket);
    Sample sample = victim.sample(referenceRunMetadata());
    assertThat(sample.name()).isEqualTo(TestInputs.referenceSample());
    assertThat(sample.lanes()).hasSize(1);
    Lane lane = sample.lanes().get(0);
    assertThat(lane.firstOfPairPath()).isEqualTo(firstBlob.getName());
    assertThat(lane.secondOfPairPath()).isEqualTo(secondBlob.getName());
}