JAL-2738 don't set AF as feature score

[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 de2f18a..5ba5d93 100644 (file)
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -835,33 +835,6 @@ public class VCFLoader
   }
 
   /**
-   * A convenience method to get the AF value for the given alternate allele
-   * index
-   * 
-   * @param variant
-   * @param alleleIndex
-   * @return
-   */
-  protected float getAlleleFrequency(VariantContext variant, int alleleIndex)
-  {
-    float score = 0f;
-    String attributeValue = getAttributeValue(variant,
-            ALLELE_FREQUENCY_KEY, alleleIndex);
-    if (attributeValue != null)
-    {
-      try
-      {
-        score = Float.parseFloat(attributeValue);
-      } catch (NumberFormatException e)
-      {
-        // leave as 0
-      }
-    }
-
-    return score;
-  }
-
-  /**
    * A convenience method to get an attribute value for an alternate allele
    * 
    * @param variant
@@ -981,10 +954,8 @@ public class VCFLoader
       type = getOntologyTerm(consequence);
     }
 
-    float score = getAlleleFrequency(variant, altAlleleIndex);
-
     SequenceFeature sf = new SequenceFeature(type, alleles, featureStart,
-            featureEnd, score, FEATURE_GROUP_VCF);
+            featureEnd, FEATURE_GROUP_VCF);
     sf.setSource(sourceId);
 
     sf.setValue(Gff3Helper.ALLELES, alleles);