X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fhtsjdk%2FVCFReaderTest.java;h=befdab1399520e88c745399c9146e6ff341cf4ed;hb=e9a1c2c372f4bbf6cf658de3dba73ef326b20c20;hp=42c655d296de47e85270d5fc0722ecec3828d417;hpb=f943e5b7a7a5ce2b819495f83dbad28028a9a956;p=jalview.git

diff --git a/test/jalview/ext/htsjdk/VCFReaderTest.java b/test/jalview/ext/htsjdk/VCFReaderTest.java
index 42c655d..befdab1 100644
--- a/test/jalview/ext/htsjdk/VCFReaderTest.java
+++ b/test/jalview/ext/htsjdk/VCFReaderTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.htsjdk;
 
 import static org.testng.Assert.assertEquals;
@@ -16,8 +36,7 @@ import org.testng.annotations.Test;
 
 public class VCFReaderTest
 {
-  private static final String[] VCF = new String[] {
-      "##fileformat=VCFv4.2",
+  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
@@ -26,8 +45,11 @@ 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
    */
@@ -99,15 +121,14 @@ public class VCFReaderTest
     File f = File.createTempFile("Test", "vcf");
     f.deleteOnExit();
     PrintWriter pw = new PrintWriter(f);
-    for (String vcfLine : VCF) {
+    for (String vcfLine : VCF)
+    {
       pw.println(vcfLine);
     }
     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
    * specified interval
@@ -121,7 +142,7 @@ public class VCFReaderTest
      * 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
@@ -131,15 +152,69 @@ 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();
+  }
 }