Increase stringency of AnnotationStep

bbimber · bbimber · commit 8caf38e5da7d · 2023-10-26T08:43:38.000-07:00
diff --git a/mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java b/mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java
@@ -574,6 +574,8 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
                 needToSubsetToInterval = false;
             }
 
+            options.add("--throw-on-missing-fields");
+
             final List<String> liftFields = Arrays.asList("LiftedContig", "LiftedStart", "LiftedStop", "ReverseComplementedAlleles");
 
             if (useFuncotator)

Original file line number	Diff line number	Diff line change
`@@ -574,6 +574,8 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno`
`574`	`574`	`needToSubsetToInterval = false;`
`575`	`575`	`}`
`576`	`576`
	`577`	`+ options.add("--throw-on-missing-fields");`
	`578`	`+`
`577`	`579`	`final List<String> liftFields = Arrays.asList("LiftedContig", "LiftedStart", "LiftedStop", "ReverseComplementedAlleles");`
`578`	`580`
`579`	`581`	`if (useFuncotator)`