+++ /dev/null
-package jalview.ext.htsjdk;
-
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertFalse;
-import static org.testng.Assert.assertTrue;
-import htsjdk.samtools.util.CloseableIterator;
-import htsjdk.variant.variantcontext.Allele;
-import htsjdk.variant.variantcontext.VariantContext;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.util.List;
-
-import org.testng.annotations.Test;
-
-public class VCFReaderTest
-{
- private static final String[] VCF = new String[] {
- "##fileformat=VCFv4.2",
- "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",
- "20\t3\t.\tC\tG\t.\tPASS\tDP=100", // SNP C/G
- "20\t7\t.\tG\tGA\t.\tPASS\tDP=100", // insertion G/GA
- "18\t2\t.\tACG\tA\t.\tPASS\tDP=100" }; // deletion ACG/A
-
- // gnomAD exome variant dataset
- private static final String VCF_PATH = "/Volumes/gjb/smacgowan/NOBACK/resources/gnomad/gnomad.exomes.r2.0.1.sites.vcf.gz";
-
- // "https://storage.cloud.google.com/gnomad-public/release/2.0.1/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz";
-
- /**
- * A test to exercise some basic functionality of the htsjdk VCF reader,
- * reading from a non-index VCF file
- *
- * @throws IOException
- */
- @Test(groups = "Functional")
- public void testReadVcf_plain() throws IOException
- {
- File f = writeVcfFile();
- VCFReader reader = new VCFReader(f.getAbsolutePath());
- CloseableIterator<VariantContext> variants = reader.iterator();
-
- /*
- * SNP C/G variant
- */
- VariantContext vc = variants.next();
- assertTrue(vc.isSNP());
- Allele ref = vc.getReference();
- assertEquals(ref.getBaseString(), "C");
- List<Allele> alleles = vc.getAlleles();
- assertEquals(alleles.size(), 2);
- assertTrue(alleles.get(0).isReference());
- assertEquals(alleles.get(0).getBaseString(), "C");
- assertFalse(alleles.get(1).isReference());
- assertEquals(alleles.get(1).getBaseString(), "G");
-
- /*
- * Insertion G -> GA
- */
- vc = variants.next();
- assertFalse(vc.isSNP());
- assertTrue(vc.isSimpleInsertion());
- ref = vc.getReference();
- assertEquals(ref.getBaseString(), "G");
- alleles = vc.getAlleles();
- assertEquals(alleles.size(), 2);
- assertTrue(alleles.get(0).isReference());
- assertEquals(alleles.get(0).getBaseString(), "G");
- assertFalse(alleles.get(1).isReference());
- assertEquals(alleles.get(1).getBaseString(), "GA");
-
- /*
- * Deletion ACG -> A
- */
- vc = variants.next();
- assertFalse(vc.isSNP());
- assertTrue(vc.isSimpleDeletion());
- ref = vc.getReference();
- assertEquals(ref.getBaseString(), "ACG");
- alleles = vc.getAlleles();
- assertEquals(alleles.size(), 2);
- assertTrue(alleles.get(0).isReference());
- assertEquals(alleles.get(0).getBaseString(), "ACG");
- assertFalse(alleles.get(1).isReference());
- assertEquals(alleles.get(1).getBaseString(), "A");
-
- assertFalse(variants.hasNext());
-
- variants.close();
- reader.close();
- }
-
- /**
- * Creates a temporary file to be read by the htsjdk VCF reader
- *
- * @return
- * @throws IOException
- */
- protected File writeVcfFile() throws IOException
- {
- File f = File.createTempFile("Test", "vcf");
- f.deleteOnExit();
- PrintWriter pw = new PrintWriter(f);
- for (String vcfLine : VCF) {
- pw.println(vcfLine);
- }
- pw.close();
- return f;
- }
-
- /**
- * A 'test' that demonstrates querying an indexed VCF file for features in a
- * specified interval
- *
- * @throws IOException
- */
- @Test
- public void testQuery_indexed() throws IOException
- {
- /*
- * if not specified, assumes index file is filename.tbi
- */
- VCFReader reader = new VCFReader(VCF_PATH);
-
- /*
- * gene NMT1 (human) is on chromosome 17
- * GCHR38 (Ensembl): 45051610-45109016
- * GCHR37 (gnoMAD): 43128978-43186384
- * CDS begins at offset 9720, first CDS variant at offset 9724
- */
- CloseableIterator<VariantContext> features = reader.query("17",
- 43128978 + 9724, 43128978 + 9734); // first 11 CDS positions
-
- assertEquals(printNext(features), 43138702);
- assertEquals(printNext(features), 43138704);
- assertEquals(printNext(features), 43138707);
- assertEquals(printNext(features), 43138708);
- assertEquals(printNext(features), 43138710);
- assertEquals(printNext(features), 43138711);
- assertFalse(features.hasNext());
-
- features.close();
- reader.close();
- }
-
- /**
- * Prints the toString value of the next variant, and returns its start
- * location
- *
- * @param features
- * @return
- */
- protected int printNext(CloseableIterator<VariantContext> features)
- {
- VariantContext next = features.next();
- System.out.println(next.toString());
- return next.getStart();
- }
-
- // "https://storage.cloud.google.com/gnomad-public/release/2.0.1/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz";
-
- /**
- * Test the query method that wraps a non-indexed VCF file
- *
- * @throws IOException
- */
- @Test(groups = "Functional")
- public void testQuery_plain() throws IOException
- {
- File f = writeVcfFile();
- VCFReader reader = new VCFReader(f.getAbsolutePath());
-
- /*
- * query for overlap of 5-8 - should find variant at 7
- */
- CloseableIterator<VariantContext> variants = reader.query("20", 5, 8);
-
- /*
- * INDEL G/GA variant
- */
- VariantContext vc = variants.next();
- assertTrue(vc.isIndel());
- assertEquals(vc.getStart(), 7);
- assertEquals(vc.getEnd(), 7);
- Allele ref = vc.getReference();
- assertEquals(ref.getBaseString(), "G");
- List<Allele> alleles = vc.getAlleles();
- assertEquals(alleles.size(), 2);
- assertTrue(alleles.get(0).isReference());
- assertEquals(alleles.get(0).getBaseString(), "G");
- assertFalse(alleles.get(1).isReference());
- assertEquals(alleles.get(1).getBaseString(), "GA");
-
- assertFalse(variants.hasNext());
-
- variants.close();
- reader.close();
- }
-}
git://source.jalview.org / jalview.git / blobdiff