Add logging

BimberLab · Jul 25, 2024 · 84e5bd3 · 84e5bd3
1 parent d5232a2
commit 84e5bd3
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/...nceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MergeVcfsAndGenotypesHandler.java b/...nceAnalysis/src/org/labkey/sequenceanalysis/run/variant/MergeVcfsAndGenotypesHandler.java
@@ -110,6 +110,10 @@ public void processFilesRemote(List<SequenceOutputFile> inputFiles, JobContext c
                     SequencePipelineService.get().sortVcf(f, null, genome.getSequenceDictionary(), ctx.getLogger());
                 }
             }
+            else
+            {
+                ctx.getLogger().debug("Pre-sorting will not be performed");
+            }
 
             action.addOutput(outputVcf, "Combined VCF", false);
             SequenceOutputFile so = new SequenceOutputFile();