Package htsjdk.variant.vcf

Examples of htsjdk.variant.vcf.VCFCodec.decode()

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        final FileInputStream s = new FileInputStream(outputVCF);
        final LineIterator lineIterator = codec.makeSourceFromStream(new PositionalBufferedStream(s));
        codec.readHeader(lineIterator);
        final String line = lineIterator.next();
        Assert.assertFalse(line == null);
        final VariantContext vc = codec.decode(line);
        Assert.assertTrue(vc.isBiallelic());
        Assert.assertTrue(vc.getReference().basesMatch("ATGTATG"));
        Assert.assertTrue(vc.getAlternateAllele(0).basesMatch("A"));
    }
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            Assert.assertFalse(line == null);
            final VariantContext vc = codec.decode(line);

            final String lineAnn = lineIteratorAnn.next();
            Assert.assertFalse(lineAnn == null);
            final VariantContext vcAnn = codecAnn.decode(lineAnn);

            Assert.assertTrue(vc.hasAttribute("FS"));
            Assert.assertTrue(vcAnn.hasAttribute("FS"));
            Assert.assertEquals(vc.getAttributeAsDouble("FS", 0.0), vcAnn.getAttributeAsDouble("FS", -1.0));
        }
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            Assert.assertFalse(line == null);
            final VariantContext vc = codec.decode(line);

            final String lineAnn = lineIteratorAnn.next();
            Assert.assertFalse(lineAnn == null);
            final VariantContext vcAnn = codecAnn.decode(lineAnn);

      Assert.assertTrue(vc.hasAttribute("QD"));
      Assert.assertTrue(vcAnn.hasAttribute("QD"));
        }
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