Fix problem when annotating Delly2 VCF files (#88)

Closes: #88 Related-Issue: #88 Projected-Results-Impact: none
varfish-org · Dec 30, 2022 · 6d37581 · 6d37581
1 parent f226257
commit 6d37581
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Showing 2 changed files with 7 additions and 11 deletions.
diff --git a/...-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsVcf.java b/...-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsVcf.java
@@ -628,18 +628,18 @@ private void annotateSvVcf(
     // Get list of filter values to skip.
     final ImmutableSet skipFilters = ImmutableSet.copyOf(args.getSkipFilters().split(","));
 
-    final String defaultSvMethod;
+    final String svMethod;
     if (callerSupport.getSvCaller() == SvCaller.GENERIC && !args.getDefaultSvMethod().equals(".")) {
-      defaultSvMethod = args.getDefaultSvMethod();
+      svMethod = args.getDefaultSvMethod();
     } else {
-      defaultSvMethod = callerSupport.getSvMethod(reader);
+      svMethod = callerSupport.getSvMethod(reader);
     }
 
     // Helpers for building record for `.gts.tsv` and `.feature-effects.tsv` records.
     final GtRecordBuilder gtRecordBuilder =
         new GtRecordBuilder(
             args.getRelease(),
-            defaultSvMethod,
+            svMethod,
             args.getOptOutFeatures(),
             args.getCaseId(),
             args.getSetId(),

diff --git a/...ore/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/GtRecordBuilder.java b/...ore/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/GtRecordBuilder.java
@@ -19,7 +19,7 @@ public class GtRecordBuilder {
   public static final String FEATURE_CALLERS_ARRAY = "callers-array";
 
   private final String release;
-  private final String defaultSvMethod;
+  private final String svMethod;
   private final String optOutFeatures;
   private final String caseId;
   private final String setId;
@@ -28,14 +28,14 @@ public class GtRecordBuilder {
 
   public GtRecordBuilder(
       String release,
-      String defaultSvMethod,
+      String svMethod,
       String optOutFeatures,
       String caseId,
       String setId,
       Pedigree pedigree,
       CallerSupport callerSupport) {
     this.release = release;
-    this.defaultSvMethod = defaultSvMethod;
+    this.svMethod = svMethod;
     this.optOutFeatures = optOutFeatures;
     this.caseId = caseId;
     this.setId = setId;
@@ -88,10 +88,6 @@ public GenotypeRecord buildRecord(
     builder.setSetId(setId);
     builder.setSvUuid(variantId.toString());
 
-    String svMethod = ctx.getCommonInfo().getAttributeAsString("SVMETHOD", null);
-    if (svMethod == null) {
-      svMethod = defaultSvMethod == null ? "." : defaultSvMethod;
-    }
     builder.setCaller(svMethod);
     if (!".".equals(svMethod)) {
       builder.setCallers(ImmutableList.of(svMethod));