delete file before move

bbimber · bbimber · commit 607779f2a341 · 2021-05-22T14:28:01.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PangolinHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/analysis/PangolinHandler.java
@@ -268,6 +268,11 @@ public static String[] runPangolin(File consensusFasta, Logger log, PipelineOutp
         try
         {
             File outputMoved = getRenamedPangolinOutput(consensusFasta);
+            if (outputMoved.exists())
+            {
+                outputMoved.delete();
+            }
+
             FileUtils.moveFile(output, outputMoved);
             try (CSVReader reader = new CSVReader(Readers.getReader(outputMoved)))
             {

Original file line number	Diff line number	Diff line change
`@@ -268,6 +268,11 @@ public static String[] runPangolin(File consensusFasta, Logger log, PipelineOutp`
`268`	`268`	`try`
`269`	`269`	`{`
`270`	`270`	`File outputMoved = getRenamedPangolinOutput(consensusFasta);`
	`271`	`+ if (outputMoved.exists())`
	`272`	`+ {`
	`273`	`+ outputMoved.delete();`
	`274`	`+ }`
	`275`	`+`
`271`	`276`	`FileUtils.moveFile(output, outputMoved);`
`272`	`277`	`try (CSVReader reader = new CSVReader(Readers.getReader(outputMoved)))`
`273`	`278`	`{`