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Quick pass of FindBugs 'method invokes inefficient Number constructor' fixes.

This commit is contained in:
Eric Banks 2012-08-08 14:34:16 -04:00
parent 4b2e3cec0b
commit a0196c9f5b
4 changed files with 3 additions and 4 deletions
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1
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -309,7 +309,6 @@ public class VariantContextAdaptors {
int index = hapmap.getStart() - ref.getWindow().getStart(); int index = hapmap.getStart() - ref.getWindow().getStart();
if ( index < 0 ) if ( index < 0 )
return null; // we weren't given enough reference context to create the VariantContext return null; // we weren't given enough reference context to create the VariantContext
Byte refBaseForIndel = new Byte(ref.getBases()[index]);
HashSet<Allele> alleles = new HashSet<Allele>(); HashSet<Allele> alleles = new HashSet<Allele>();
Allele refSNPAllele = Allele.create(ref.getBase(), true); Allele refSNPAllele = Allele.create(ref.getBase(), true);

2
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
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@ -1304,7 +1304,7 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
@Override @Override
public Integer reduceInit() { public Integer reduceInit() {
return new Integer(0); return 0;
} }

2
public/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java
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@ -329,7 +329,7 @@ public class SequenceDictionaryUtils {
*/ */
private static class CompareSequenceRecordsByIndex implements Comparator<SAMSequenceRecord> { private static class CompareSequenceRecordsByIndex implements Comparator<SAMSequenceRecord> {
public int compare(SAMSequenceRecord x, SAMSequenceRecord y) { public int compare(SAMSequenceRecord x, SAMSequenceRecord y) {
return new Integer(x.getSequenceIndex()).compareTo(y.getSequenceIndex()); return Integer.valueOf(x.getSequenceIndex()).compareTo(y.getSequenceIndex());
} }
} }

2
public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java
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@ -223,7 +223,7 @@ public class QualQuantizer {
@Override @Override
public int compareTo(final QualInterval qualInterval) { public int compareTo(final QualInterval qualInterval) {
return new Integer(this.qStart).compareTo(qualInterval.qStart); return Integer.valueOf(this.qStart).compareTo(qualInterval.qStart);
} }
/** /**