From abf6b0aacd117ee1e2ae04cb019cfa8d2b7b4f12 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 3 Oct 2017 11:21:52 +0100
Subject: [PATCH] JAL-2738 update test for threaded VCFLoader

---
 test/jalview/io/vcf/VCFLoaderTest.java |   34 ++++++++++++++++++++++++++++----
 1 file changed, 30 insertions(+), 4 deletions(-)

diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java
index 7379ecd..b01266e 100644
--- a/test/jalview/io/vcf/VCFLoaderTest.java
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -1,6 +1,7 @@
 package jalview.io.vcf;
 
 import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.fail;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -50,14 +51,14 @@ public class VCFLoaderTest
       "17\t45051613\t.\tG\tGA,C\t1666.64\tRF\tAC=15;AF=3.08130e-03" };
 
   @Test(groups = "Functional")
-  public void testLoadVCF() throws IOException
+  public void testDoLoad() throws IOException
   {
     AlignmentI al = buildAlignment();
     VCFLoader loader = new VCFLoader(al);
 
     File f = makeVcf();
 
-    loader.loadVCF(f.getPath(), null);
+    loader.doLoad(f.getPath(), null);
 
     /*
      * verify variant feature(s) added to gene
@@ -211,7 +212,7 @@ public class VCFLoaderTest
    * @throws IOException
    */
   @Test(groups = "Functional")
-  public void testLoadVCF_reverseStrand() throws IOException
+  public void testDoLoad_reverseStrand() throws IOException
   {
     AlignmentI al = buildAlignment();
 
@@ -219,7 +220,7 @@ public class VCFLoaderTest
 
     File f = makeVcf();
 
-    loader.loadVCF(f.getPath(), null);
+    loader.doLoad(f.getPath(), null);
 
     /*
      * verify variant feature(s) added to gene2
@@ -284,4 +285,29 @@ public class VCFLoaderTest
     assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
     assertEquals(sf.getDescription(), "p.Ala6Gly");
   }
+
+  /**
+   * Tests that where variant records have more than one SNP allele, a variant
+   * feature is created for each, and the corresponding data values set on it
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testDoLoad_multipleAlleles() throws IOException
+  {
+    fail("todo");
+  }
+
+  /**
+   * Tests that if VEP consequence (CSQ) data is present in the VCF data, then
+   * it is added to the variant feature, but restricted where possible to the
+   * consequences for a specific transcript
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testDoLoad_vepCsq() throws IOException
+  {
+    fail("todo");
+  }
 }
-- 
1.7.10.2