Ejemplos de VCFFileReader.iterator en Java

Ejemplo n.º 1

Archivo: AbstractVCFCodecTest.java Proyecto: magicDGS/htsjdk

  @Test
  public void shouldPreserveSymbolicAlleleCase() {
    VCFFileReader reader =
        new VCFFileReader(new File(VariantBaseTest.variantTestDataRoot + "breakpoint.vcf"), false);
    VariantContext variant = reader.iterator().next();
    reader.close();

    // VCF v4.1 s1.4.5
    // Tools processing VCF files are not required to preserve case in the allele String, except for
    // IDs, which are case sensitive.
    Assert.assertTrue(variant.getAlternateAllele(0).getDisplayString().contains("chr12"));
  }