public static VariantBuilder newBuilder(String str) { return new VariantBuilder(str); }
public static VariantBuilder newBuilder() { return new VariantBuilder(); }
public static VariantBuilder newBuilder(String chromosome, Integer start, Integer end, String reference, String alternate) { return new VariantBuilder(chromosome, start, end, reference, alternate); }
/** * Creates a variant parsing a string. * * Format : (chr):(start)[-(end)][:(ref)]:(alt) * * @see VariantBuilder * @param variantString Variant string * @throws IllegalArgumentException if the variant does not match with the pattern */ public Variant(String variantString) { this(); new VariantBuilder(variantString).build(this); }
public static Variant parseVariant(String variantString) { return new VariantBuilder(variantString).build(); }
private Variant(String chromosome, int start, @Nullable Integer end, String reference, String alternate, String strand) { this(); // Nullable end. The builder will infer the end (and length) if null. new VariantBuilder(chromosome, start, end, reference, alternate).setStrand(strand).build(this); }
public Variant(String chromosome, int start, int end, String reference, String alternate, String strand) { this(); new VariantBuilder(chromosome, start, end, reference, alternate).setStrand(strand).build(this); }
VariantBuilder builder = new VariantBuilder(chromosome, start, end, reference, alternate);
@Test public void isRefVariantTest() throws Exception { assertTrue(VariantToVcfSliceConverterTask.isRefVariant(new VariantBuilder("1:100:A:C").setFormat("GT").addSample("S1", "0/0").build())); assertTrue(VariantToVcfSliceConverterTask.isRefVariant(new VariantBuilder("1:100:A:C").setFormat("GT").addSample("S1", "0/0").addSample("S2", "0").build())); assertFalse(VariantToVcfSliceConverterTask.isRefVariant(new VariantBuilder("1:100:A:C").setFormat("GT").addSample("S1", "0/0").addSample("S2", "0/1").build())); assertFalse(VariantToVcfSliceConverterTask.isRefVariant(new VariantBuilder("1:100:A:C").setFormat("GT").addSample("S1", "0/1").addSample("S2", "0/0").build())); assertFalse(VariantToVcfSliceConverterTask.isRefVariant(new VariantBuilder("1:100:A:C").setFormat("GT").addSample("S1", "0/1").addSample("S2", "0/1").build())); assertFalse(VariantToVcfSliceConverterTask.isRefVariant(new VariantBuilder("1:100:A:C").setFormat("GT").addSample("S1", "./.").build())); } }