@Test
public void testGetAnnotationsForUnTrimmedDeletionReturnsValueOfAllelePositionTrim() {

    //Given a single allele from a multi-positional site, they might not be fully trimmed. In cases where there is repetition, depending on the program used, the final
    // variant allele will be different.
      VCF:      X-118887583-TCAAAA-TCAAAACAAAA
      Exomiser: X-118887583-T     -TCAAAA
      CellBase: X-118887584--     - CAAAA
      Jannovar: X-118887588-      -      CAAAA
      Nirvana:  X-118887589-      -      CAAAA
    //trimming first with Exomiser, then annotating with Jannovar, constrains the Jannovar annotation to the same position as Exomiser.
      VCF:      X-118887583-TCAAAA-TCAAAACAAAA
      Exomiser: X-118887583-T     -TCAAAA
      CellBase: X-118887584--     - CAAAA
      Jannovar: X-118887583-      - CAAAA      (Jannovar is zero-based)
      Nirvana:  X-118887584-      - CAAAA
      Cellbase:
      https://github.com/opencb/biodata/blob/develop/biodata-tools/src/main/java/org/opencb/biodata/tools/variant/VariantNormalizer.java
      http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/v4/hsapiens/genomic/variant/X:118887583:TCAAAA:TCAAAACAAAA/annotation?assembly=grch37&limit=-1&skip=-1&count=false&Output format=json&normalize=true
      Nirvana style trimming:
      https://github.com/Illumina/Nirvana/blob/master/VariantAnnotation/Algorithms/BiDirectionalTrimmer.cs
      Jannovar:
      https://github.com/charite/jannovar/blob/master/jannovar-core/src/main/java/de/charite/compbio/jannovar/reference/VariantDataCorrector.java
    int pos = 118608470;
    String ref = "AGTT";
    String alt = "AGT";
    VariantAnnotation annotations = instance.annotate("X", pos, ref, alt);
    System.out.println(annotations);
    AllelePosition allelePosition = AllelePosition.trim(pos, ref, alt);
    System.out.printf("AnnotationList{pos=%d, ref='%s', alt='%s'}%n", annotations.getPosition(), annotations.getRef(), annotations
            .getAlt());
    System.out.println(allelePosition);
    assertThat(annotations.getChromosome(), equalTo(23));
    assertThat(annotations.getPosition(), equalTo(allelePosition.getPos()));
    assertThat(annotations.getRef(), equalTo(allelePosition.getRef()));
    assertThat(annotations.getAlt(), equalTo(allelePosition.getAlt()));
    assertThat(annotations.hasTranscriptAnnotations(), is(false));
}