Update KING --ped to --fam

bbimber · bbimber · commit c4366597cd98 · 2025-02-13T10:45:02.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java
@@ -172,7 +172,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
             }
 
             File kingFam = createFamFile(pedFile, new File(plinkOutBed.getParentFile(), "plink.fam"));
-            kingArgs.add("--ped");
+            kingArgs.add("--fam");
             kingArgs.add(kingFam.getPath());
 
             output.addIntermediateFile(kingFam);

Original file line number	Diff line number	Diff line change
`@@ -172,7 +172,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno`
`172`	`172`	`}`
`173`	`173`
`174`	`174`	`File kingFam = createFamFile(pedFile, new File(plinkOutBed.getParentFile(), "plink.fam"));`
`175`		`- kingArgs.add("--ped");`
	`175`	`+ kingArgs.add("--fam");`
`176`	`176`	`kingArgs.add(kingFam.getPath());`
`177`	`177`
`178`	`178`	`output.addIntermediateFile(kingFam);`