Compute kinship using both KING and plink's implementation of KING

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/KingInferenceStep.java

@@ -139,7 +139,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         plinkArgs1.add("--out");
         plinkArgs1.add(plinkOut.getPath());
 
-        plink.execute(plinkArgs);
+        plink.execute(plinkArgs1);
 
         File plinkOutBed = new File(plinkOut.getPath() + ".bed");
         if (!plinkOutBed.exists())
@@ -154,7 +154,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         plinkArgs2.add("--out");
         plinkArgs2.add(plinkOutKing.getPath());
 
-        plink.execute(plinkArgs1);
+        plink.execute(plinkArgs2);
 
         File plinkOutKingFile = new File(plinkOut.getPath() + ".kin0");
         if (!plinkOutKingFile.exists())