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

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index 421cf38..9d98b7e 100644 (file)
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -556,7 +556,15 @@ public class VCFLoader
       return 0;
     }
 
-    return addVcfVariants(seq, reader, vcfMap, vcfAssembly);
+    /*
+     * work with the dataset sequence here
+     */
+    SequenceI dss = seq.getDatasetSequence();
+    if (dss == null)
+    {
+      dss = seq;
+    }
+    return addVcfVariants(dss, reader, vcfMap, vcfAssembly);
   }
 
   /**
@@ -892,10 +900,24 @@ public class VCFLoader
     String allele = alt.getBaseString();
 
     /*
+     * insertion after a genomic base, if on reverse strand, has to be 
+     * converted to insertion of complement after the preceding position 
+     */
+    int referenceLength = reference.length();
+    if (!forwardStrand && allele.length() > referenceLength
+            && allele.startsWith(reference))
+    {
+      featureStart -= referenceLength;
+      featureEnd = featureStart;
+      char insertAfter = seq.getCharAt(featureStart - seq.getStart());
+      reference = Dna.reverseComplement(String.valueOf(insertAfter));
+      allele = allele.substring(referenceLength) + reference;
+    }
+
+    /*
      * build the ref,alt allele description e.g. "G,A", using the base
      * complement if the sequence is on the reverse strand
      */
-    // FIXME correctly handle insertions on reverse strand JAL-2845
     StringBuilder sb = new StringBuilder();
     sb.append(forwardStrand ? reference : Dna.reverseComplement(reference));
     sb.append(COMMA);

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