JAL-2845 locate reverse strand insertion as complement insertion at a preceding position

[jalview.git] / test / jalview / io / vcf / VCFLoaderTest.java

diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java
index 246337d..29cf9c9 100644 (file)
--- a/test/jalview/io/vcf/VCFLoaderTest.java
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -321,69 +321,89 @@ public class VCFLoaderTest
 
     /*
      * 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));
 
-    sf = geneFeatures.get(1);
+    /*
+     * variant A/T at 45051611 maps to T/A at gene position 24
+     */
+    SequenceFeature sf = geneFeatures.get(3);
     assertEquals(sf.getFeatureGroup(), "VCF");
-    assertEquals(sf.getBegin(), 22);
-    assertEquals(sf.getEnd(), 22);
+    assertEquals(sf.getBegin(), 24);
+    assertEquals(sf.getEnd(), 24);
     assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getScore(), 3.0e-03, DELTA);
-    assertEquals("C,TC", sf.getValue(Gff3Helper.ALLELES));
+    assertEquals(sf.getScore(), 5.0e-03, DELTA);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "T,A");
 
+    /*
+     * variant A/C at 45051611 maps to T/G at gene position 24
+     */
     sf = geneFeatures.get(2);
     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.getValue(Gff3Helper.ALLELES), "T,G");
 
-    sf = geneFeatures.get(3);
+    /*
+     * variant G/C at 45051613 maps to C/G at gene position 22
+     */
+    sf = geneFeatures.get(1);
     assertEquals(sf.getFeatureGroup(), "VCF");
-    assertEquals(sf.getBegin(), 24);
-    assertEquals(sf.getEnd(), 24);
+    assertEquals(sf.getBegin(), 22);
+    assertEquals(sf.getEnd(), 22);
     assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getScore(), 5.0e-03, DELTA);
-    assertEquals("T,A", sf.getValue(Gff3Helper.ALLELES));
+    assertEquals(sf.getScore(), 2.0e-03, DELTA);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "C,G");
+
+    /*
+     * 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(0);
+    assertEquals(sf.getFeatureGroup(), "VCF");
+    assertEquals(sf.getBegin(), 21);
+    assertEquals(sf.getEnd(), 21);
+    assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
+    assertEquals(sf.getScore(), 3.0e-03, DELTA);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GT");
 
     /*
-     * 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 2 variant features added to transcript2
      */
     List<SequenceFeature> transcriptFeatures = al.getSequenceAt(3)
             .getSequenceFeatures();
     assertEquals(transcriptFeatures.size(), 2);
+
+    /*
+     * insertion G/GT at position 21 of gene maps to position 16 of transcript
+     */
     sf = transcriptFeatures.get(0);
     assertEquals(sf.getFeatureGroup(), "VCF");
-    assertEquals(sf.getBegin(), 17);
-    assertEquals(sf.getEnd(), 17);
+    assertEquals(sf.getBegin(), 16);
+    assertEquals(sf.getEnd(), 16);
     assertEquals(sf.getType(), SequenceOntologyI.SEQUENCE_VARIANT);
-    assertEquals(sf.getScore(), 2.0e-03, DELTA);
-    assertEquals("C,G", sf.getValue(Gff3Helper.ALLELES));
+    assertEquals(sf.getScore(), 3.0e-03, DELTA);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "G,GT");
 
+    /*
+     * SNP C/G at position 22 of gene maps to position 17 of transcript
+     */
     sf = transcriptFeatures.get(1);
     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.getScore(), 2.0e-03, DELTA);
+    assertEquals(sf.getValue(Gff3Helper.ALLELES), "C,G");
 
     /*
      * verify variant feature(s) computed and added to protein