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Other random FindBugs fixes

This commit is contained in:
Eric Banks 2012-08-08 14:56:27 -04:00
parent f652d7806e
commit 0a2a646a52
4 changed files with 7 additions and 9 deletions
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1
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -263,7 +263,6 @@ public class UnifiedArgumentCollection {
uac.referenceSampleName = referenceSampleName;
uac.samplePloidy = samplePloidy;
uac.maxQualityScore = minQualityScore;
uac.maxQualityScore = maxQualityScore;
uac.phredScaledPrior = phredScaledPrior;
uac.minPower = minPower;
uac.minReferenceDepth = minReferenceDepth;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
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@ -34,15 +34,13 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.Arrays;
import java.util.Collection;
import java.util.Map;
import java.util.Set;
import java.util.*;
/**
* Filters a lifted-over VCF file for ref bases that have been changed.
@ -66,7 +64,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : null, samples);
final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : Collections.<VCFHeaderLine>emptySet(), samples);
writer.writeHeader(vcfHeader);
}

2
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
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@ -492,6 +492,6 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
}
private final void error(final String message) throws RuntimeException {
throw new UserException.MalformedBCF2(String.format("At record %d with position %d:", recordNo, pos, message));
throw new UserException.MalformedBCF2(String.format("%s, at record %d with position %d:", message, recordNo, pos));
}
}

5
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java
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@ -401,10 +401,11 @@ public class RecalDatumNode<T extends RecalDatum> {
if ( minPenaltyNode == null || minPenaltyNode.getSecond() > maxPenalty ) {
// nothing to merge, or the best candidate is above our max allowed
if ( minPenaltyNode == null )
if ( minPenaltyNode == null ) {
if ( logger.isDebugEnabled() ) logger.debug("Stopping because no candidates could be found");
else
} else {
if ( logger.isDebugEnabled() ) logger.debug("Stopping because node " + minPenaltyNode.getFirst() + " has penalty " + minPenaltyNode.getSecond() + " > max " + maxPenalty);
}
break;
} else {
// remove the lowest penalty element, and continue