X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fhtsjdk%2FVCFReaderTest.java;fp=test%2Fjalview%2Fext%2Fhtsjdk%2FVCFReaderTest.java;h=0000000000000000000000000000000000000000;hb=4f77328104498504339216829abf5ea87e2791ec;hp=bf617aec97ba4293decec6a3bab85cd05d2b3d99;hpb=2b8c0785318a3528e1876e8e2dd48b7d831eae69;p=jalview.git

diff --git a/test/jalview/ext/htsjdk/VCFReaderTest.java b/test/jalview/ext/htsjdk/VCFReaderTest.java
deleted file mode 100644
index bf617ae..0000000
--- a/test/jalview/ext/htsjdk/VCFReaderTest.java
+++ /dev/null
@@ -1,200 +0,0 @@
-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();
-  }
-}