Bugfix to nimble align

bbimber · bbimber · commit cf3b7dcb0d42 · 2022-01-09T06:48:11.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleAligner.java b/singlecell/src/org/labkey/singlecell/run/NimbleAligner.java
@@ -95,21 +95,21 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu
             output.addIntermediateFiles(crOutput.getIntermediateFiles());
 
             // Remove the whole 10x folder:
-            output.addIntermediateFile(output.getBAM().getParentFile().getParentFile());
+            output.addIntermediateFile(crOutput.getBAM().getParentFile().getParentFile());
 
             try
             {
                 if (localBam.exists())
                 {
                     localBam.delete();
                 }
-                FileUtils.copyFile(output.getBAM(), localBam);
+                FileUtils.copyFile(crOutput.getBAM(), localBam);
 
                 if (localBamIdx.exists())
                 {
                     localBamIdx.delete();
                 }
-                FileUtils.copyFile(new File(output.getBAM().getPath() + ".bai"), localBamIdx);
+                FileUtils.copyFile(new File(crOutput.getBAM().getPath() + ".bai"), localBamIdx);
             }
             catch (IOException e)
             {

Original file line number	Diff line number	Diff line change
`@@ -95,21 +95,21 @@ public AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nu`
`95`	`95`	`output.addIntermediateFiles(crOutput.getIntermediateFiles());`
`96`	`96`
`97`	`97`	`// Remove the whole 10x folder:`
`98`		`- output.addIntermediateFile(output.getBAM().getParentFile().getParentFile());`
	`98`	`+ output.addIntermediateFile(crOutput.getBAM().getParentFile().getParentFile());`
`99`	`99`
`100`	`100`	`try`
`101`	`101`	`{`
`102`	`102`	`if (localBam.exists())`
`103`	`103`	`{`
`104`	`104`	`localBam.delete();`
`105`	`105`	`}`
`106`		`- FileUtils.copyFile(output.getBAM(), localBam);`
	`106`	`+ FileUtils.copyFile(crOutput.getBAM(), localBam);`
`107`	`107`
`108`	`108`	`if (localBamIdx.exists())`
`109`	`109`	`{`
`110`	`110`	`localBamIdx.delete();`
`111`	`111`	`}`
`112`		`- FileUtils.copyFile(new File(output.getBAM().getPath() + ".bai"), localBamIdx);`
	`112`	`+ FileUtils.copyFile(new File(crOutput.getBAM().getPath() + ".bai"), localBamIdx);`
`113`	`113`	`}`
`114`	`114`	`catch (IOException e)`
`115`	`115`	`{`