Method test

src/test/java/com/rtg/vcf/VcfRecordTest.java:50–99

()

  }

  public void test() {
    final VcfRecord rec = new VcfRecord("chr1", 1209, "a");
    rec.setId(".")
      .setQuality("12.8")
      .addAltCall("c")
      .addAltCall("t")
      .addFilter("TEST1")
      .addFilter("TEST2")
      .setInfo("DP", "23")
      .setInfo("TEST", "45", "46", "47", "48")
      .setNumberOfSamples(2)
      .addFormatAndSample("GT", "0/0")
      .addFormatAndSample("GT", "0/1")
      .addFormatAndSample("GQ", "100")
      .addFormatAndSample("GQ", "95")
    ;

    assertEquals("chr1", rec.getSequenceName());
    assertEquals(1210, rec.getOneBasedStart());
    assertEquals(".", rec.getId());
    assertEquals("a", rec.getRefCall());
    assertEquals("c", rec.getAltCalls().get(0));
    assertEquals("t", rec.getAltCalls().get(1));
    assertEquals("TEST1", rec.getFilters().get(0));
    assertEquals("TEST2", rec.getFilters().get(1));
    assertEquals("12.8", rec.getQuality());
    assertEquals("23", rec.getInfo("DP"));
    final Iterator<String> iter = Arrays.asList(rec.getInfoSplit("TEST")).iterator();
    assertEquals("45", iter.next());
    assertEquals("46", iter.next());
    assertEquals("47", iter.next());
    assertEquals("48", iter.next());
    assertEquals("0/0", rec.getFormat("GT").get(0));
    assertEquals("0/1", rec.getFormat("GT").get(1));
    assertEquals("100", rec.getFormat("GQ").get(0));
    assertEquals("95", rec.getFormat("GQ").get(1));
    final String line = ""
      + "chr1" + TAB
      + "1210" + TAB
      + "." + TAB
      + "a" + TAB
      + "c,t" + TAB
      + "12.8" + TAB
      + "TEST1;TEST2" + TAB
      + "DP=23;TEST=45,46,47,48" + TAB
      + "GT:GQ" + TAB
      + "0/0:100" + TAB
      + "0/1:95";
    assertEquals(line, rec.toString());
  }

  public void testError2() {
    try {