Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

[jalview.git] / test / jalview / ext / htsjdk / VCFReaderTest.java

diff --git a/test/jalview/ext/htsjdk/VCFReaderTest.java b/test/jalview/ext/htsjdk/VCFReaderTest.java
index 42c655d..bf617ae 100644 (file)
--- a/test/jalview/ext/htsjdk/VCFReaderTest.java
+++ b/test/jalview/ext/htsjdk/VCFReaderTest.java
@@ -26,8 +26,11 @@ public class VCFReaderTest
   // 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
+   * A test to exercise some basic functionality of the htsjdk VCF reader,
+   * reading from a non-index VCF file
    * 
    * @throws IOException
    */
@@ -105,8 +108,6 @@ public class VCFReaderTest
     pw.close();
     return f;
   }
-
-  // "https://storage.cloud.google.com/gnomad-public/release/2.0.1/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz";
   
   /**
    * A 'test' that demonstrates querying an indexed VCF file for features in a
@@ -131,15 +132,69 @@ public class VCFReaderTest
     CloseableIterator<VariantContext> features = reader.query("17",
             43128978 + 9724, 43128978 + 9734); // first 11 CDS positions
 
-    assertEquals(features.next().getStart(), 43138702);
-    assertEquals(features.next().getStart(), 43138704);
-    assertEquals(features.next().getStart(), 43138707);
-    assertEquals(features.next().getStart(), 43138708);
-    assertEquals(features.next().getStart(), 43138710);
-    assertEquals(features.next().getStart(), 43138711);
+    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();
+  }
 }