Bugfix to GatherVcfsCloud

BimberLab · Feb 23, 2025 · 02e696e · 02e696e
1 parent 474d362
commit 02e696e
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Showing 2 changed files with 11 additions and 1 deletion.
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GatherVcfsCloudWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/GatherVcfsCloudWrapper.java
@@ -2,6 +2,7 @@
 
 import org.apache.logging.log4j.Logger;
 import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
 import org.labkey.api.sequenceanalysis.run.AbstractGatk4Wrapper;
 import org.labkey.api.writer.PrintWriters;
 
@@ -40,5 +41,14 @@ public void gatherVcfs(File output, List<File> inputVcfs) throws PipelineJobExce
         execute(args);
 
         argFile.delete();
+
+        try
+        {
+            SequenceAnalysisService.get().ensureVcfIndex(output, getLogger());
+        }
+        catch (IOException e)
+        {
+            throw new PipelineJobException(e);
+        }
     }
 }
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/SequenceUtil.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/util/SequenceUtil.java
@@ -480,7 +480,7 @@ public static File combineVcfs(List<File> files, ReferenceGenome genome, File ou
             File idx = new File(outputGzip.getPath() + ".tbi");
             if (!idx.exists())
             {
-                throw new PipelineJobException("Unable to find output: " + idx.getPath());
+                throw new PipelineJobException("Unable to find index: " + idx.getPath());
             }
 
             if (showTotals)