JAL-3576 IntervalStore updated to v1.2

diff --git a/j11lib/intervalstore-v1.1.jar b/j11lib/intervalstore-v1.1.jar
deleted file mode 100644 (file)
index 668b543..0000000
Binary files a/j11lib/intervalstore-v1.1.jar and /dev/null differ

diff --git a/j11lib/intervalstore-v1.2.jar b/j11lib/intervalstore-v1.2.jar
new file mode 100644 (file)
index 0000000..fdd0ee7
Binary files /dev/null and b/j11lib/intervalstore-v1.2.jar differ

diff --git a/j8lib/intervalstore-v1.1.jar b/j8lib/intervalstore-v1.1.jar
deleted file mode 100644 (file)
index 668b543..0000000
Binary files a/j8lib/intervalstore-v1.1.jar and /dev/null differ

diff --git a/j8lib/intervalstore-v1.2.jar b/j8lib/intervalstore-v1.2.jar
new file mode 100644 (file)
index 0000000..fdd0ee7
Binary files /dev/null and b/j8lib/intervalstore-v1.2.jar differ

diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java
index a719cc4..c8dd8f0 100644 (file)
--- a/test/jalview/io/vcf/VCFLoaderTest.java
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -5,6 +5,16 @@ import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertTrue;
 
+import java.io.File;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -20,16 +30,6 @@ import jalview.io.FileLoader;
 import jalview.io.gff.Gff3Helper;
 import jalview.util.MapList;
 
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintWriter;
-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
 {
   private static final float DELTA = 0.00001f;
@@ -119,10 +119,24 @@ public class VCFLoaderTest
             .getSequenceFeatures();
     SequenceFeatures.sortFeatures(geneFeatures, true);
     assertEquals(geneFeatures.size(), 5);
+
     SequenceFeature sf = geneFeatures.get(0);
     assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 2);
     assertEquals(sf.getEnd(), 2);
+    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(1);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 2);
+    assertEquals(sf.getEnd(), 2);
     assertEquals(sf.getScore(), 0f);
     assertEquals(sf.getValue("AF"), "4.0e-03");
     assertEquals(sf.getValue("AF_AFR"), "2.3e-4");
@@ -135,28 +149,17 @@ public class VCFLoaderTest
     // 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(), 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(), SEQUENCE_VARIANT);
     assertEquals(sf.getScore(), 0f);
-    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
             DELTA);
-    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA");
+    assertNull(sf.getValue("ID")); // '.' is ignored
+    assertNull(sf.getValue("FILTER")); // '.' is ignored
 
     sf = geneFeatures.get(3);
     assertEquals(sf.getFeatureGroup(), "VCF");
@@ -164,11 +167,9 @@ public class VCFLoaderTest
     assertEquals(sf.getEnd(), 4);
     assertEquals(sf.getType(), SEQUENCE_VARIANT);
     assertEquals(sf.getScore(), 0f);
-    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
             DELTA);
-    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA");
-    assertNull(sf.getValue("ID")); // '.' is ignored
-    assertNull(sf.getValue("FILTER")); // '.' is ignored
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
 
     sf = geneFeatures.get(4);
     assertEquals(sf.getFeatureGroup(), "VCF");
@@ -186,24 +187,26 @@ public class VCFLoaderTest
     List<SequenceFeature> transcriptFeatures = al.getSequenceAt(1)
             .getSequenceFeatures();
     assertEquals(transcriptFeatures.size(), 3);
+    
     sf = transcriptFeatures.get(0);
     assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 2);
     assertEquals(sf.getEnd(), 2);
     assertEquals(sf.getType(), SEQUENCE_VARIANT);
     assertEquals(sf.getScore(), 0f);
-    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
             DELTA);
-    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA");
+    
     sf = transcriptFeatures.get(1);
     assertEquals(sf.getFeatureGroup(), "VCF");
     assertEquals(sf.getBegin(), 2);
     assertEquals(sf.getEnd(), 2);
     assertEquals(sf.getType(), SEQUENCE_VARIANT);
     assertEquals(sf.getScore(), 0f);
-    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 3.0e-03,
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 2.0e-03,
             DELTA);
-    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GA");
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,C");
 
     /*
      * verify SNP variant feature(s) computed and added to protein
@@ -413,7 +416,7 @@ public class VCFLoaderTest
             DELTA);
 
     /*
-     * variant A/C at 45051611 maps to T/G at gene position 24
+     * variant A/T at 45051611 maps to T/A at gene position 24
      */
     sf = geneFeatures.get(3);
     assertEquals(sf.getFeatureGroup(), "VCF");
@@ -421,12 +424,12 @@ public class VCFLoaderTest
     assertEquals(sf.getEnd(), 24);
     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,
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "T,A");
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 5.0e-03,
             DELTA);
 
     /*
-     * variant A/T at 45051611 maps to T/A at gene position 24
+     * variant A/C at 45051611 maps to T/G at gene position 24
      */
     sf = geneFeatures.get(4);
     assertEquals(sf.getFeatureGroup(), "VCF");
@@ -434,8 +437,8 @@ public class VCFLoaderTest
     assertEquals(sf.getEnd(), 24);
     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,
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "T,G");
+    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 4.0e-03,
             DELTA);
 
     /*
@@ -557,8 +560,8 @@ public class VCFLoaderTest
     assertEquals(sf.getBegin(), 13);
     assertEquals(sf.getEnd(), 13);
     assertEquals(sf.getScore(), 0f);
-    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.5f, DELTA);
-    assertEquals(sf.getValue("alleles"), "C,T");
+    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);
 
@@ -566,8 +569,8 @@ public class VCFLoaderTest
     assertEquals(sf.getBegin(), 13);
     assertEquals(sf.getEnd(), 13);
     assertEquals(sf.getScore(), 0f);
-    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.4f, DELTA);
-    assertEquals(sf.getValue("alleles"), "C,G");
+    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);
 
@@ -575,8 +578,8 @@ public class VCFLoaderTest
     assertEquals(sf.getBegin(), 17);
     assertEquals(sf.getEnd(), 17);
     assertEquals(sf.getScore(), 0f);
-    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA);
-    assertEquals(sf.getValue("alleles"), "A,G");
+    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);
 
@@ -584,8 +587,8 @@ public class VCFLoaderTest
     assertEquals(sf.getBegin(), 17);
     assertEquals(sf.getEnd(), 17); // insertion
     assertEquals(sf.getScore(), 0f);
-    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA);
-    assertEquals(sf.getValue("alleles"), "A,AC");
+    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);
 
@@ -614,8 +617,9 @@ public class VCFLoaderTest
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
     assertEquals(sf.getScore(), 0f);
-    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA);
-    assertEquals(sf.getValue("alleles"), "A,G");
+    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);
     assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
 
@@ -623,8 +627,9 @@ public class VCFLoaderTest
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
     assertEquals(sf.getScore(), 0f);
-    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA);
-    assertEquals(sf.getValue("alleles"), "A,AC");
+    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);
     assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
 
@@ -675,8 +680,9 @@ public class VCFLoaderTest
     assertEquals(sf.getBegin(), 7);
     assertEquals(sf.getEnd(), 7);
     assertEquals(sf.getScore(), 0f);
-    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.5f, DELTA);
-    assertEquals(sf.getValue("alleles"), "C,T");
+    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);
     assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
 
@@ -684,8 +690,9 @@ public class VCFLoaderTest
     assertEquals(sf.getBegin(), 7);
     assertEquals(sf.getEnd(), 7);
     assertEquals(sf.getScore(), 0f);
-    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.4f, DELTA);
-    assertEquals(sf.getValue("alleles"), "C,G");
+    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);
     assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
 
@@ -693,8 +700,9 @@ public class VCFLoaderTest
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
     assertEquals(sf.getScore(), 0f);
-    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.7f, DELTA);
-    assertEquals(sf.getValue("alleles"), "A,G");
+    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);
     assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
 
@@ -702,8 +710,9 @@ public class VCFLoaderTest
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
     assertEquals(sf.getScore(), 0f);
-    assertEquals(Float.parseFloat((String) sf.getValue("AF")), 0.6f, DELTA);
-    assertEquals(sf.getValue("alleles"), "A,AC");
+    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);
     assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
   }