@Test
public void testAnnotateSpliceAcceptorVariant() {

    // This transcript is on the negative strand
    // TranscriptModel Gene=FGFR2 accession=uc021pzz.1 Chr10 Strand=- seqLen=4654
    // txRegion=123237843-123357972(120129 bases) CDS=123239370-123353331(113961 bases)
    VariantAnnotation annotations = instance.annotate("10", 123243319, "T", "G");
    assertThat(annotations.getChromosomeName(), equalTo("10"));
    assertThat(annotations.getChromosome(), equalTo(10));
    assertThat(annotations.getPosition(), equalTo(123243319));
    assertThat(annotations.getRef(), equalTo("T"));
    assertThat(annotations.getAlt(), equalTo("G"));
    assertThat(annotations.getGeneId(), equalTo("2263"));
    assertThat(annotations.getGeneSymbol(), equalTo("FGFR2"));
    assertThat(annotations.getVariantEffect(), equalTo(VariantEffect.SPLICE_ACCEPTOR_VARIANT));
    assertThat(annotations.hasTranscriptAnnotations(), is(true));
    TranscriptAnnotation transcriptAnnotation = annotations.getTranscriptAnnotations().get(0);
    assertThat(transcriptAnnotation.getGeneSymbol(), equalTo("FGFR2"));
    assertThat(transcriptAnnotation.getAccession(), equalTo("uc021pzz.1"));
    assertThat(transcriptAnnotation.getDistanceFromNearestGene(), equalTo(Integer.MIN_VALUE));
    assertThat(transcriptAnnotation.getHgvsGenomic(), equalTo("g.12291429A>C"));
    assertThat(transcriptAnnotation.getHgvsCdna(), equalTo("c.2196-2A>C"));
    assertThat(transcriptAnnotation.getHgvsProtein(), equalTo("p.?"));
}