Correct location of BAM for vireo

bbimber · bbimber · commit 2bb4aec17997 · 2024-03-06T11:19:43.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/VireoHandler.java
@@ -102,7 +102,7 @@ private File getBarcodesFile(File loupe)
 
         private File getBamFile(File loupe)
         {
-            File[] files = loupe.getParentFile().getParentFile().listFiles(f -> f.getName().endsWith(".bam"));
+            File[] files = loupe.getParentFile().listFiles(f -> f.getName().endsWith(".bam"));
             if (files == null || files.length == 0)
             {
                 throw new IllegalArgumentException("Unable to find BAM file for Loupe file");

Original file line number	Diff line number	Diff line change
`@@ -102,7 +102,7 @@ private File getBarcodesFile(File loupe)`
`102`	`102`
`103`	`103`	`private File getBamFile(File loupe)`
`104`	`104`	`{`
`105`		`- File[] files = loupe.getParentFile().getParentFile().listFiles(f -> f.getName().endsWith(".bam"));`
	`105`	`+ File[] files = loupe.getParentFile().listFiles(f -> f.getName().endsWith(".bam"));`
`106`	`106`	`if (files == null \|\| files.length == 0)`
`107`	`107`	`{`
`108`	`108`	`throw new IllegalArgumentException("Unable to find BAM file for Loupe file");`