Correct arguments to BcftoolsFillTagsStep

bbimber · bbimber · commit 961ab8c78cef · 2024-01-24T13:49:10.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/BcftoolsFillTagsStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/BcftoolsFillTagsStep.java
@@ -100,6 +100,7 @@ public VariantProcessingStep.Output processVariants(File inputVCF, File outputDi
             throw new PipelineJobException("No annotations were selected");
         }
 
+        options.add("--");
         options.add("-t");
         options.add(StringUtils.join(annotations, ","));
 

Original file line number	Diff line number	Diff line change
`@@ -100,6 +100,7 @@ public VariantProcessingStep.Output processVariants(File inputVCF, File outputDi`
`100`	`100`	`throw new PipelineJobException("No annotations were selected");`
`101`	`101`	`}`
`102`	`102`
	`103`	`+ options.add("--");`
`103`	`104`	`options.add("-t");`
`104`	`105`	`options.add(StringUtils.join(annotations, ","));`
`105`	`106`