Bugfix to bbmap

bbimber · bbimber · commit 38b2b53405dd · 2025-05-17T16:01:22.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BBMapWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/alignment/BBMapWrapper.java
@@ -94,6 +94,12 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
             File refDir = new File(getPipelineCtx().getWorkingDirectory(), "ref");
             try
             {
+                if (refDir.exists())
+                {
+                    getPipelineCtx().getLogger().debug("Deleting existing ref dir: " + refDir);
+                    FileUtils.deleteDirectory(refDir);
+                }
+
                 FileUtils.moveDirectory(localIdx, refDir);
             }
             catch (IOException e)

Original file line number	Diff line number	Diff line change
`@@ -94,6 +94,12 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu`
`94`	`94`	`File refDir = new File(getPipelineCtx().getWorkingDirectory(), "ref");`
`95`	`95`	`try`
`96`	`96`	`{`
	`97`	`+ if (refDir.exists())`
	`98`	`+ {`
	`99`	`+ getPipelineCtx().getLogger().debug("Deleting existing ref dir: " + refDir);`
	`100`	`+ FileUtils.deleteDirectory(refDir);`
	`101`	`+ }`
	`102`	`+`
`97`	`103`	`FileUtils.moveDirectory(localIdx, refDir);`
`98`	`104`	`}`
`99`	`105`	`catch (IOException e)`