From 8377424089f5186b659fe712b870c1fc2e74dd2e Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 21 May 2011 13:43:48 +0000
Subject: [PATCH] Basic error checking to ensure incoming arguments are
 provided correctly.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5831 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/genotyper/GenotypeLikelihoodsCalculationModel.java | 2 ++
 .../genotyper/SNPGenotypeLikelihoodsCalculationModel.java      | 3 +++
 .../sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java   | 3 ++-
 3 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
index b083f6ae3..8bb544c77 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
@@ -32,6 +32,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
@@ -63,6 +64,7 @@ public abstract class GenotypeLikelihoodsCalculationModel implements Cloneable {
      * @param UAC           unified arg collection
      */
     protected GenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
+        if ( logger == null || UAC == null ) throw new ReviewedStingException("Bad arguments");
         this.UAC = UAC.clone();
         this.logger = logger;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index 59e339376..50015fd95 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -30,6 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -55,6 +56,8 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
     }
 
     public static VariantContext getSNPVCFromAllelesRod(RefMetaDataTracker tracker, ReferenceContext ref, boolean requireSNP, Logger logger) {
+        if ( tracker == null || ref == null || logger == null )
+            throw new ReviewedStingException("Bad arguments: tracker=" + tracker + " ref=" + ref + " logger=" + logger);
         VariantContext vc = null;
 
         // search for usable record
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index d7b611759..06b4aacd2 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -99,7 +99,8 @@ public class UnifiedGenotyperEngine {
         else
             samples = SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader());
 
-        initialize(UAC, null, null, null, samples.size());
+        final Logger logger = Logger.getLogger(UnifiedGenotyperEngine.class);
+        initialize(UAC, logger, null, null, samples.size());
     }
 
     public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, PrintStream verboseWriter, VariantAnnotatorEngine engine, Set<String> samples) {