X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvcf%2FVCFLoader.java;h=1abe638517229ba40c740a542987159edbd34866;hb=refs%2Fheads%2Fspike%2Fclinvar;hp=d6a530b7956a086a11c8c8d406e65d0f8b088327;hpb=6875edc608179e9710388439099542296f263c15;p=jalview.git

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index d6a530b..1abe638 100644
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -257,9 +257,9 @@ public class VCFLoader
   private Set<String> badData;
 
   /**
-   * Constructor given a VCF file
+   * Constructor given a path to a VCF file
    * 
-   * @param alignment
+   * @param vcfFile
    */
   public VCFLoader(String vcfFile)
   {
@@ -922,7 +922,11 @@ public class VCFLoader
   }
 
   /**
-   * A convenience method to get an attribute value for an alternate allele
+   * A convenience method to get an attribute value for an alternate allele.
+   * {@code alleleIndex} is the position in the list of values for the allele.
+   * If {@alleleIndex == -1} then all values are concatenated (comma-separated).
+   * This is the case for fields declared with "Number=." i.e. values are not
+   * related to specific alleles.
    * 
    * @param variant
    * @param attributeName
@@ -934,16 +938,25 @@ public class VCFLoader
   {
     Object att = variant.getAttribute(attributeName);
 
+    String result = null;
     if (att instanceof String)
     {
-      return (String) att;
+      result = (String) att;
     }
-    else if (att instanceof ArrayList)
+    else if (att instanceof List<?>)
     {
-      return ((List<String>) att).get(alleleIndex);
+      List<String> theList = (List<String>) att;
+      if (alleleIndex == -1)
+      {
+        result = StringUtils.listToDelimitedString(theList, ",");
+      }
+      else
+      {
+        result = theList.get(alleleIndex);
+      }
     }
 
-    return null;
+    return result;
   }
 
   /**
@@ -1332,6 +1345,10 @@ public class VCFLoader
          */
         index++;
       }
+      else if (number == VCFHeaderLineCount.UNBOUNDED) // .
+      {
+        index = -1;
+      }
       else if (number != VCFHeaderLineCount.A)
       {
         /*