Bugfix to KING/plink2

bbimber · bbimber · commit 4f5323581648 · 2025-02-14T17:04:45.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java
@@ -156,7 +156,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
 
         plink.execute(plinkArgs2);
 
-        File plinkOutKingFile = new File(plinkOut.getPath() + ".kin0");
+        File plinkOutKingFile = new File(plinkOutKing.getPath() + ".kin0");
         if (!plinkOutKingFile.exists())
         {
             throw new PipelineJobException("Unable to find file: " + plinkOutKingFile.getPath());

Original file line number	Diff line number	Diff line change
`@@ -156,7 +156,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno`
`156`	`156`
`157`	`157`	`plink.execute(plinkArgs2);`
`158`	`158`
`159`		`- File plinkOutKingFile = new File(plinkOut.getPath() + ".kin0");`
	`159`	`+ File plinkOutKingFile = new File(plinkOutKing.getPath() + ".kin0");`
`160`	`160`	`if (!plinkOutKingFile.exists())`
`161`	`161`	`{`
`162`	`162`	`throw new PipelineJobException("Unable to find file: " + plinkOutKingFile.getPath());`