+
+ /**
+ * A test that demonstrates loading a contig sequence from an indexed sequence
+ * database which is the reference for a VCF file
+ *
+ * @throws IOException
+ */
+ @Test(groups = "Functional")
+ public void testLoadVCFContig() throws IOException
+ {
+ VCFLoader loader = new VCFLoader(
+ "test/jalview/io/vcf/testVcf2.vcf");
+
+ SequenceI seq = loader.loadVCFContig("contig123");
+ assertEquals(seq.getLength(), 15);
+ assertEquals(seq.getSequenceAsString(), "AAAAACCCCCGGGGG");
+ List<SequenceFeature> features = seq.getSequenceFeatures();
+ SequenceFeatures.sortFeatures(features, true);
+ assertEquals(features.size(), 2);
+ SequenceFeature sf = features.get(0);
+ assertEquals(sf.getBegin(), 8);
+ assertEquals(sf.getEnd(), 8);
+ assertEquals(sf.getDescription(), "C,A");
+ sf = features.get(1);
+ assertEquals(sf.getBegin(), 12);
+ assertEquals(sf.getEnd(), 12);
+ assertEquals(sf.getDescription(), "G,T");
+
+ seq = loader.loadVCFContig("contig789");
+ assertEquals(seq.getLength(), 25);
+ assertEquals(seq.getSequenceAsString(), "GGGGGTTTTTAAAAACCCCCGGGGG");
+ features = seq.getSequenceFeatures();
+ SequenceFeatures.sortFeatures(features, true);
+ assertEquals(features.size(), 2);
+ sf = features.get(0);
+ assertEquals(sf.getBegin(), 2);
+ assertEquals(sf.getEnd(), 2);
+ assertEquals(sf.getDescription(), "G,T");
+ sf = features.get(1);
+ assertEquals(sf.getBegin(), 21);
+ assertEquals(sf.getEnd(), 21);
+ assertEquals(sf.getDescription(), "G,A");
+
+ seq = loader.loadVCFContig("contig456");
+ assertEquals(seq.getLength(), 20);
+ assertEquals(seq.getSequenceAsString(), "CCCCCGGGGGTTTTTAAAAA");
+ features = seq.getSequenceFeatures();
+ SequenceFeatures.sortFeatures(features, true);
+ assertEquals(features.size(), 1);
+ sf = features.get(0);
+ assertEquals(sf.getBegin(), 15);
+ assertEquals(sf.getEnd(), 15);
+ assertEquals(sf.getDescription(), "T,C");
+ }
+}
\ No newline at end of file