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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
This commit is contained in:
depristo 2011-05-21 13:43:48 +00:00
parent e234589240
commit 8377424089
3 changed files with 7 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
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@ -32,6 +32,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.Allele;
import org.broadinstitute.sting.utils.BaseUtils; 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.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@ -63,6 +64,7 @@ public abstract class GenotypeLikelihoodsCalculationModel implements Cloneable {
* @param UAC unified arg collection * @param UAC unified arg collection
*/ */
protected GenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) { protected GenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
if ( logger == null || UAC == null ) throw new ReviewedStingException("Bad arguments");
this.UAC = UAC.clone(); this.UAC = UAC.clone();
this.logger = logger; this.logger = logger;
} }

3
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -30,6 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils; import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.baq.BAQ; 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.exceptions.StingException;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype; import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; 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) { 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; VariantContext vc = null;
// search for usable record // search for usable record

3
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -99,7 +99,8 @@ public class UnifiedGenotyperEngine {
else else
samples = SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()); 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) { public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC, Logger logger, PrintStream verboseWriter, VariantAnnotatorEngine engine, Set<String> samples) {