X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2Fvcf%2FVCFLoaderTest.java;h=a719cc4369e96de615b9562a94587579420e8946;hb=5e6d487896b10a77ee0240b764c82c42aeeaf6aa;hp=246337d6e8f9dfcf784e0e401b95ad8c649267b0;hpb=779411693812e6e3ad6c547e44f1e58124263ffd;p=jalview.git

diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java
index 246337d..a719cc4 100644
--- a/test/jalview/io/vcf/VCFLoaderTest.java
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -1,6 +1,9 @@
 package jalview.io.vcf;
 
+import static jalview.io.gff.SequenceOntologyI.SEQUENCE_VARIANT;
 import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
+import static org.testng.Assert.assertTrue;
 
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
@@ -9,12 +12,12 @@ import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureAttributes;
 import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.AlignFrame;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 import jalview.io.gff.Gff3Helper;
-import jalview.io.gff.SequenceOntologyI;
 import jalview.util.MapList;
 
 import java.io.File;
@@ -24,6 +27,7 @@ import java.util.List;
 import java.util.Map;
 
 import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeTest;
 import org.testng.annotations.Test;
 
 public class VCFLoaderTest
@@ -56,17 +60,23 @@ public class VCFLoaderTest
           + ">transcript4/1-18\n-----TGG-GGACGAGAGTGTGA-A\n";
 
   private static final String[] VCF = { "##fileformat=VCFv4.2",
+      // fields other than AF are ignored when parsing as they have no INFO definition
       "##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">",
+      "##INFO=<ID=AC_Female,Number=A,Type=Integer,Description=\"Allele count in Female genotypes\"",
+      "##INFO=<ID=AF_AFR,Number=A,Type=Float,Description=\"Allele Frequency among African/African American genotypes\"",
       "##reference=Homo_sapiens/GRCh38",
       "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",
       // A/T,C variants in position 2 of gene sequence (precedes transcript)
-      // should create 2 variant features with respective scores
-      "17\t45051611\t.\tA\tT,C\t1666.64\tRF\tAC=15;AF=5.0e-03,4.0e-03",
+      // should create 2 variant features with respective AF values
+      // malformed values for AC_Female and AF_AFR should be ignored
+      "17\t45051611\trs384765\tA\tT,C\t1666.64\tRF;XYZ\tAC=15;AF=5.0e-03,4.0e-03;AC_Female=12,3d;AF_AFR=low,2.3e-4",
       // SNP G/C in position 4 of gene sequence, position 2 of transcript
       // insertion G/GA is transferred to nucleotide but not to peptide
-      "17\t45051613\t.\tG\tGA,C\t1666.64\tRF\tAC=15;AF=3.0e-03,2.0e-03" };
+      "17\t45051613\t.\tG\tGA,C\t1666.65\t.\tAC=15;AF=3.0e-03,2.0e-03",
+      // '.' in INFO field should be ignored
+      "17\t45051615\t.\tG\tC\t1666.66\tRF\tAC=16;AF=." };
 
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public void setUp()
   {
     /*
@@ -75,17 +85,28 @@ public class VCFLoaderTest
     Cache.loadProperties("test/jalview/io/testProps.jvprops");
     Cache.setProperty("VCF_FIELDS", ".*");
     Cache.setProperty("VEP_FIELDS", ".*");
+    Cache.setProperty("VCF_ASSEMBLY", "GRCh38=GRCh38");
+    Cache.initLogger();
+  }
+
+  @BeforeTest(alwaysRun = true)
+  public void setUpBeforeTest()
+  {
+    /*
+     * clear down feature attributes metadata
+     */
+    FeatureAttributes.getInstance().clear();
   }
 
   @Test(groups = "Functional")
   public void testDoLoad() throws IOException
   {
     AlignmentI al = buildAlignment();
-    VCFLoader loader = new VCFLoader(al);
 
-    File f = makeVcf();
+    File f = makeVcfFile();
+    VCFLoader loader = new VCFLoader(f.getPath());
 
-    loader.doLoad(f.getPath(), null);
+    loader.doLoad(al.getSequencesArray(), null);
 
     /*
      * verify variant feature(s) added to gene
@@ -97,64 +118,98 @@ public class VCFLoaderTest
     List<SequenceFeature> geneFeatures = al.getSequenceAt(0)
             .getSequenceFeatures();
     SequenceFeatures.sortFeatures(geneFeatures, true);
-    assertEquals(geneFeatures.size(), 4);
+    assertEquals(geneFeatures.size(), 5);
     SequenceFeature sf = geneFeatures.get(0);
     assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 2);
     assertEquals(sf.getEnd(), 2);
-    assertEquals(sf.getScore(), 4.0e-03, DELTA);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(sf.getValue("AF"), "4.0e-03");
+    assertEquals(sf.getValue("AF_AFR"), "2.3e-4");
     assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,C");
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getType(), SEQUENCE_VARIANT);
+    assertEquals(sf.getValue("POS"), "45051611");
+    assertEquals(sf.getValue("ID"), "rs384765");
+    assertEquals(sf.getValue("QUAL"), "1666.64");
+    assertEquals(sf.getValue("FILTER"), "RF;XYZ");
+    // malformed integer for AC_Female is ignored (JAL-3375)
+    assertNull(sf.getValue("AC_Female"));
+
     sf = geneFeatures.get(1);
     assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 2);
     assertEquals(sf.getEnd(), 2);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getScore(), 5.0e-03, DELTA);
+    assertEquals(sf.getType(), SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 5.0e-03,
+            DELTA);
+    assertEquals(sf.getValue("AC_Female"), "12");
+    // malformed float for AF_AFR is ignored (JAL-3375)
+    assertNull(sf.getValue("AC_AFR"));
     assertEquals(sf.getValue(Gff3Helper.ALLELES), "A,T");
 
     sf = geneFeatures.get(2);
     assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 4);
     assertEquals(sf.getEnd(), 4);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getScore(), 2.0e-03, DELTA);
+    assertEquals(sf.getType(), SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+            DELTA);
     assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
 
     sf = geneFeatures.get(3);
     assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 4);
     assertEquals(sf.getEnd(), 4);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getScore(), 3.0e-03, DELTA);
+    assertEquals(sf.getType(), SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+            DELTA);
     assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA");
+    assertNull(sf.getValue("ID")); // '.' is ignored
+    assertNull(sf.getValue("FILTER")); // '.' is ignored
+
+    sf = geneFeatures.get(4);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 6);
+    assertEquals(sf.getEnd(), 6);
+    assertEquals(sf.getType(), SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 0f);
+    // AF=. should not have been captured
+    assertNull(sf.getValue("AF"));
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
 
     /*
      * verify variant feature(s) added to transcript
      */
     List<SequenceFeature> transcriptFeatures = al.getSequenceAt(1)
             .getSequenceFeatures();
-    assertEquals(transcriptFeatures.size(), 2);
+    assertEquals(transcriptFeatures.size(), 3);
     sf = transcriptFeatures.get(0);
     assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 2);
     assertEquals(sf.getEnd(), 2);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getScore(), 2.0e-03, DELTA);
+    assertEquals(sf.getType(), SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+            DELTA);
     assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
     sf = transcriptFeatures.get(1);
     assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 2);
     assertEquals(sf.getEnd(), 2);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getScore(), 3.0e-03, DELTA);
+    assertEquals(sf.getType(), SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+            DELTA);
     assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA");
 
     /*
      * verify SNP variant feature(s) computed and added to protein
      * first codon AGC varies to ACC giving S/T
      */
-    DBRefEntry[] dbRefs = al.getSequenceAt(1).getDBRefs();
+    List<DBRefEntry> dbRefs = al.getSequenceAt(1).getDBRefs();
     SequenceI peptide = null;
     for (DBRefEntry dbref : dbRefs)
     {
@@ -164,16 +219,14 @@ public class VCFLoaderTest
       }
     }
     List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures();
-    assertEquals(proteinFeatures.size(), 1);
-    sf = proteinFeatures.get(0);
-    assertEquals(sf.getFeatureGroup(), "VCF");
-    assertEquals(sf.getBegin(), 1);
-    assertEquals(sf.getEnd(), 1);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getDescription(), "p.Ser1Thr");
+
+    /*
+     * JAL-3187 don't precompute protein features, do dynamically instead
+     */
+    assertTrue(proteinFeatures.isEmpty());
   }
 
-  private File makeVcf() throws IOException
+  private File makeVcfFile() throws IOException
   {
     File f = File.createTempFile("Test", ".vcf");
     f.deleteOnExit();
@@ -313,83 +366,116 @@ public class VCFLoaderTest
   {
     AlignmentI al = buildAlignment();
 
-    VCFLoader loader = new VCFLoader(al);
+    File f = makeVcfFile();
 
-    File f = makeVcf();
+    VCFLoader loader = new VCFLoader(f.getPath());
 
-    loader.doLoad(f.getPath(), null);
+    loader.doLoad(al.getSequencesArray(), null);
 
     /*
      * verify variant feature(s) added to gene2
-     * gene/1-25 maps to chromosome 45051634- reverse strand
-     * variants A/T, A/C at 45051611 and G/GA,G/C at 45051613 map to
-     * T/A, T/G and C/TC,C/G at gene positions 24 and 22 respectively
+     * gene2/1-25 maps to chromosome 45051634- reverse strand
      */
     List<SequenceFeature> geneFeatures = al.getSequenceAt(2)
             .getSequenceFeatures();
     SequenceFeatures.sortFeatures(geneFeatures, true);
-    assertEquals(geneFeatures.size(), 4);
-    SequenceFeature sf = geneFeatures.get(0);
-    assertEquals(sf.getFeatureGroup(), "VCF");
-    assertEquals(sf.getBegin(), 22);
-    assertEquals(sf.getEnd(), 22);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getScore(), 2.0e-03, DELTA);
-    assertEquals("C,G", sf.getValue(Gff3Helper.ALLELES));
+    assertEquals(geneFeatures.size(), 5);
+    SequenceFeature sf;
 
+    /*
+     * insertion G/GA at 45051613 maps to an insertion at
+     * the preceding position (21) on reverse strand gene
+     * reference: CAAGC -> GCTTG/21-25
+     * genomic variant: CAAGAC (G/GA)
+     * gene variant: GTCTTG (G/GT at 21)
+     */
     sf = geneFeatures.get(1);
     assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 21);
+    assertEquals(sf.getEnd(), 21);
+    assertEquals(sf.getType(), SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GT");
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+            DELTA);
+
+    /*
+     * variant G/C at 45051613 maps to C/G at gene position 22
+     */
+    sf = geneFeatures.get(2);
+    assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 22);
     assertEquals(sf.getEnd(), 22);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getScore(), 3.0e-03, DELTA);
-    assertEquals("C,TC", sf.getValue(Gff3Helper.ALLELES));
+    assertEquals(sf.getType(), SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "C,G");
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+            DELTA);
 
-    sf = geneFeatures.get(2);
+    /*
+     * variant A/C at 45051611 maps to T/G at gene position 24
+     */
+    sf = geneFeatures.get(3);
     assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 24);
     assertEquals(sf.getEnd(), 24);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getScore(), 4.0e-03, DELTA);
-    assertEquals("T,G", sf.getValue(Gff3Helper.ALLELES));
+    assertEquals(sf.getType(), SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "T,G");
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 4.0e-03,
+            DELTA);
 
-    sf = geneFeatures.get(3);
+    /*
+     * variant A/T at 45051611 maps to T/A at gene position 24
+     */
+    sf = geneFeatures.get(4);
     assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 24);
     assertEquals(sf.getEnd(), 24);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getScore(), 5.0e-03, DELTA);
-    assertEquals("T,A", sf.getValue(Gff3Helper.ALLELES));
+    assertEquals(sf.getType(), SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "T,A");
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 5.0e-03,
+            DELTA);
 
     /*
-     * verify variant feature(s) added to transcript2
-     * variants G/GA,G/C at position 22 of gene overlap and map to
-     * C/TC,C/G at position 17 of transcript
+     * verify 3 variant features added to transcript2
      */
     List<SequenceFeature> transcriptFeatures = al.getSequenceAt(3)
             .getSequenceFeatures();
-    assertEquals(transcriptFeatures.size(), 2);
-    sf = transcriptFeatures.get(0);
-    assertEquals(sf.getFeatureGroup(), "VCF");
-    assertEquals(sf.getBegin(), 17);
-    assertEquals(sf.getEnd(), 17);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getScore(), 2.0e-03, DELTA);
-    assertEquals("C,G", sf.getValue(Gff3Helper.ALLELES));
+    assertEquals(transcriptFeatures.size(), 3);
 
+    /*
+     * insertion G/GT at position 21 of gene maps to position 16 of transcript
+     */
     sf = transcriptFeatures.get(1);
     assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 16);
+    assertEquals(sf.getEnd(), 16);
+    assertEquals(sf.getType(), SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GT");
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+            DELTA);
+
+    /*
+     * SNP C/G at position 22 of gene maps to position 17 of transcript
+     */
+    sf = transcriptFeatures.get(2);
+    assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 17);
     assertEquals(sf.getEnd(), 17);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getScore(), 3.0e-03, DELTA);
-    assertEquals("C,TC", sf.getValue(Gff3Helper.ALLELES));
+    assertEquals(sf.getType(), SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "C,G");
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+            DELTA);
 
     /*
      * verify variant feature(s) computed and added to protein
      * last codon GCT varies to GGT giving A/G in the last peptide position
      */
-    DBRefEntry[] dbRefs = al.getSequenceAt(3).getDBRefs();
+    List<DBRefEntry> dbRefs = al.getSequenceAt(3).getDBRefs();
     SequenceI peptide = null;
     for (DBRefEntry dbref : dbRefs)
     {
@@ -399,13 +485,11 @@ public class VCFLoaderTest
       }
     }
     List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures();
-    assertEquals(proteinFeatures.size(), 1);
-    sf = proteinFeatures.get(0);
-    assertEquals(sf.getFeatureGroup(), "VCF");
-    assertEquals(sf.getBegin(), 6);
-    assertEquals(sf.getEnd(), 6);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getDescription(), "p.Ala6Gly");
+
+    /*
+     * JAL-3187 don't precompute protein features, do dynamically instead
+     */
+    assertTrue(proteinFeatures.isEmpty());
   }
 
   /**
@@ -420,7 +504,7 @@ public class VCFLoaderTest
   {
     AlignmentI al = buildAlignment();
 
-    VCFLoader loader = new VCFLoader(al);
+    VCFLoader loader = new VCFLoader("test/jalview/io/vcf/testVcf.vcf");
 
     /*
      * VCF data file with variants at gene3 positions
@@ -430,7 +514,7 @@ public class VCFLoaderTest
      * 13 C/G, C/T
      * 17 A/AC (insertion), A/G
      */
-    loader.doLoad("test/jalview/io/vcf/testVcf.dat", null);
+    loader.doLoad(al.getSequencesArray(), null);
 
     /*
      * verify variant feature(s) added to gene3
@@ -442,24 +526,29 @@ public class VCFLoaderTest
     SequenceFeature sf = geneFeatures.get(0);
     assertEquals(sf.getBegin(), 1);
     assertEquals(sf.getEnd(), 1);
-    assertEquals(sf.getScore(), 0.1f, DELTA);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.1f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,A");
     // gene features include Consequence for all transcripts
     Map map = (Map) sf.getValue("CSQ");
     assertEquals(map.size(), 9);
+    assertEquals(map.get("PolyPhen"), "Bad");
 
     sf = geneFeatures.get(1);
     assertEquals(sf.getBegin(), 5);
     assertEquals(sf.getEnd(), 5);
-    assertEquals(sf.getScore(), 0.2f, DELTA);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.2f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,T");
     map = (Map) sf.getValue("CSQ");
     assertEquals(map.size(), 9);
+    assertEquals(map.get("PolyPhen"), "Bad;;"); // %3B%3B decoded
 
     sf = geneFeatures.get(2);
     assertEquals(sf.getBegin(), 9);
     assertEquals(sf.getEnd(), 11); // deletion over 3 positions
-    assertEquals(sf.getScore(), 0.3f, DELTA);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.3f, DELTA);
     assertEquals(sf.getValue("alleles"), "CGG,C");
     map = (Map) sf.getValue("CSQ");
     assertEquals(map.size(), 9);
@@ -467,7 +556,8 @@ public class VCFLoaderTest
     sf = geneFeatures.get(3);
     assertEquals(sf.getBegin(), 13);
     assertEquals(sf.getEnd(), 13);
-    assertEquals(sf.getScore(), 0.5f, DELTA);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.5f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,T");
     map = (Map) sf.getValue("CSQ");
     assertEquals(map.size(), 9);
@@ -475,7 +565,8 @@ public class VCFLoaderTest
     sf = geneFeatures.get(4);
     assertEquals(sf.getBegin(), 13);
     assertEquals(sf.getEnd(), 13);
-    assertEquals(sf.getScore(), 0.4f, DELTA);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.4f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,G");
     map = (Map) sf.getValue("CSQ");
     assertEquals(map.size(), 9);
@@ -483,7 +574,8 @@ public class VCFLoaderTest
     sf = geneFeatures.get(5);
     assertEquals(sf.getBegin(), 17);
     assertEquals(sf.getEnd(), 17);
-    assertEquals(sf.getScore(), 0.7f, DELTA);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,G");
     map = (Map) sf.getValue("CSQ");
     assertEquals(map.size(), 9);
@@ -491,7 +583,8 @@ public class VCFLoaderTest
     sf = geneFeatures.get(6);
     assertEquals(sf.getBegin(), 17);
     assertEquals(sf.getEnd(), 17); // insertion
-    assertEquals(sf.getScore(), 0.6f, DELTA);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,AC");
     map = (Map) sf.getValue("CSQ");
     assertEquals(map.size(), 9);
@@ -509,7 +602,8 @@ public class VCFLoaderTest
     sf = transcriptFeatures.get(0);
     assertEquals(sf.getBegin(), 3);
     assertEquals(sf.getEnd(), 3);
-    assertEquals(sf.getScore(), 0.2f, DELTA);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.2f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,T");
     // transcript features only have Consequence for that transcripts
     map = (Map) sf.getValue("CSQ");
@@ -519,7 +613,8 @@ public class VCFLoaderTest
     sf = transcriptFeatures.get(1);
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
-    assertEquals(sf.getScore(), 0.7f, DELTA);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,G");
     assertEquals(map.size(), 9);
     assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
@@ -527,7 +622,8 @@ public class VCFLoaderTest
     sf = transcriptFeatures.get(2);
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
-    assertEquals(sf.getScore(), 0.6f, DELTA);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,AC");
     assertEquals(map.size(), 9);
     assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
@@ -539,7 +635,7 @@ public class VCFLoaderTest
      * and GAG/GGG which is E/G in position 4
      * the insertion variant is not transferred to the peptide
      */
-    DBRefEntry[] dbRefs = al.findName("transcript3").getDBRefs();
+    List<DBRefEntry> dbRefs = al.findName("transcript3").getDBRefs();
     SequenceI peptide = null;
     for (DBRefEntry dbref : dbRefs)
     {
@@ -549,13 +645,24 @@ public class VCFLoaderTest
       }
     }
     List<SequenceFeature> proteinFeatures = peptide.getSequenceFeatures();
-    assertEquals(proteinFeatures.size(), 1);
-    sf = proteinFeatures.get(0);
-    assertEquals(sf.getFeatureGroup(), "VCF");
-    assertEquals(sf.getBegin(), 4);
-    assertEquals(sf.getEnd(), 4);
-    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getDescription(), "p.Glu4Gly");
+    /*
+     * JAL-3187 don't precompute protein features, do dynamically instead
+     */
+    assertTrue(proteinFeatures.isEmpty());
+    // SequenceFeatures.sortFeatures(proteinFeatures, true);
+    // assertEquals(proteinFeatures.size(), 2);
+    // sf = proteinFeatures.get(0);
+    // assertEquals(sf.getFeatureGroup(), "VCF");
+    // assertEquals(sf.getBegin(), 1);
+    // assertEquals(sf.getEnd(), 1);
+    // assertEquals(sf.getType(), SequenceOntologyI.SYNONYMOUS_VARIANT);
+    // assertEquals(sf.getDescription(), "agC/agT");
+    // sf = proteinFeatures.get(1);
+    // assertEquals(sf.getFeatureGroup(), "VCF");
+    // assertEquals(sf.getBegin(), 4);
+    // assertEquals(sf.getEnd(), 4);
+    // assertEquals(sf.getType(), SequenceOntologyI.NONSYNONYMOUS_VARIANT);
+    // assertEquals(sf.getDescription(), "p.Glu4Gly");
 
     /*
      * verify variant feature(s) added to transcript4
@@ -567,7 +674,8 @@ public class VCFLoaderTest
     sf = transcriptFeatures.get(0);
     assertEquals(sf.getBegin(), 7);
     assertEquals(sf.getEnd(), 7);
-    assertEquals(sf.getScore(), 0.5f, DELTA);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.5f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,T");
     assertEquals(map.size(), 9);
     assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
@@ -575,7 +683,8 @@ public class VCFLoaderTest
     sf = transcriptFeatures.get(1);
     assertEquals(sf.getBegin(), 7);
     assertEquals(sf.getEnd(), 7);
-    assertEquals(sf.getScore(), 0.4f, DELTA);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.4f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,G");
     assertEquals(map.size(), 9);
     assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
@@ -583,7 +692,8 @@ public class VCFLoaderTest
     sf = transcriptFeatures.get(2);
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
-    assertEquals(sf.getScore(), 0.7f, DELTA);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,G");
     assertEquals(map.size(), 9);
     assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
@@ -591,9 +701,64 @@ public class VCFLoaderTest
     sf = transcriptFeatures.get(3);
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
-    assertEquals(sf.getScore(), 0.6f, DELTA);
+    assertEquals(sf.getScore(), 0f);
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,AC");
     assertEquals(map.size(), 9);
     assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
   }
-}
+
+  /**
+   * A test that demonstrates loading a contig sequence from an indexed sequence
+   * database which is the reference for a VCF file
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testLoadVCFContig() throws IOException
+  {
+    VCFLoader loader = new VCFLoader(
+            "test/jalview/io/vcf/testVcf2.vcf");
+
+    SequenceI seq = loader.loadVCFContig("contig123");
+    assertEquals(seq.getLength(), 15);
+    assertEquals(seq.getSequenceAsString(), "AAAAACCCCCGGGGG");
+    List<SequenceFeature> features = seq.getSequenceFeatures();
+    SequenceFeatures.sortFeatures(features, true);
+    assertEquals(features.size(), 2);
+    SequenceFeature sf = features.get(0);
+    assertEquals(sf.getBegin(), 8);
+    assertEquals(sf.getEnd(), 8);
+    assertEquals(sf.getDescription(), "C,A");
+    sf = features.get(1);
+    assertEquals(sf.getBegin(), 12);
+    assertEquals(sf.getEnd(), 12);
+    assertEquals(sf.getDescription(), "G,T");
+
+    seq = loader.loadVCFContig("contig789");
+    assertEquals(seq.getLength(), 25);
+    assertEquals(seq.getSequenceAsString(), "GGGGGTTTTTAAAAACCCCCGGGGG");
+    features = seq.getSequenceFeatures();
+    SequenceFeatures.sortFeatures(features, true);
+    assertEquals(features.size(), 2);
+    sf = features.get(0);
+    assertEquals(sf.getBegin(), 2);
+    assertEquals(sf.getEnd(), 2);
+    assertEquals(sf.getDescription(), "G,T");
+    sf = features.get(1);
+    assertEquals(sf.getBegin(), 21);
+    assertEquals(sf.getEnd(), 21);
+    assertEquals(sf.getDescription(), "G,A");
+
+    seq = loader.loadVCFContig("contig456");
+    assertEquals(seq.getLength(), 20);
+    assertEquals(seq.getSequenceAsString(), "CCCCCGGGGGTTTTTAAAAA");
+    features = seq.getSequenceFeatures();
+    SequenceFeatures.sortFeatures(features, true);
+    assertEquals(features.size(), 1);
+    sf = features.get(0);
+    assertEquals(sf.getBegin(), 15);
+    assertEquals(sf.getEnd(), 15);
+    assertEquals(sf.getDescription(), "T,C");
+  }
+}
\ No newline at end of file