Merge branch 'feature/JAL-3121gffAttributeMap' into develop

[jalview.git] / src / jalview / io / vcf / VCFLoader.java

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index decff23..cbdd66c 100644 (file)
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -1,6 +1,5 @@
 package jalview.io.vcf;
 
-import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Dna;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.bin.Cache;
@@ -20,6 +19,7 @@ import jalview.io.gff.SequenceOntologyI;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.util.StringUtils;
 
 import java.io.File;
 import java.io.IOException;
@@ -56,6 +56,8 @@ import htsjdk.variant.vcf.VCFInfoHeaderLine;
  */
 public class VCFLoader
 {
+  private static final String VCF_ENCODABLE = ":;=%,";
+
   /*
    * Jalview feature attributes for VCF fixed column data
    */
@@ -678,7 +680,8 @@ public class VCFLoader
         /*
          * dna-to-peptide product mapping
          */
-        AlignmentUtils.computeProteinFeatures(seq, mapTo, map);
+        // JAL-3187 render on the fly instead
+        // AlignmentUtils.computeProteinFeatures(seq, mapTo, map);
       }
       else
       {
@@ -1284,14 +1287,6 @@ public class VCFLoader
       }
 
       /*
-       * filter out fields we don't want to capture
-       */
-      if (!vcfFieldsOfInterest.contains(key))
-      {
-        continue;
-      }
-
-      /*
        * we extract values for other data which are allele-specific; 
        * these may be per alternate allele (INFO[key].Number = 'A') 
        * or per allele including reference (INFO[key].Number = 'R') 
@@ -1330,6 +1325,11 @@ public class VCFLoader
       String value = getAttributeValue(variant, key, index);
       if (value != null && isValid(variant, key, value))
       {
+        /*
+         * decode colon, semicolon, equals sign, percent sign, comma (only)
+         * as required by the VCF specification (para 1.2)
+         */
+        value = StringUtils.urlDecode(value, VCF_ENCODABLE);
         addFeatureAttribute(sf, key, value);
       }
     }
@@ -1449,6 +1449,11 @@ public class VCFLoader
             String id = vepFieldsOfInterest.get(i);
             if (id != null)
             {
+              /*
+               * VCF spec requires encoding of special characters e.g. '='
+               * so decode them here before storing
+               */
+              field = StringUtils.urlDecode(field, VCF_ENCODABLE);
               csqValues.put(id, field);
             }
           }