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Another round of FindBugs fixes. Object internally stores a reference to an externally mutable array. Very dangerous.

This commit is contained in:
Ryan Poplin 2012-08-21 09:33:58 -04:00
parent 55b7949d68
commit 605acaae9c
3 changed files with 9 additions and 9 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnVertex.java
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@ -14,7 +14,7 @@ public class DeBruijnVertex {
public final int kmer; public final int kmer;
public DeBruijnVertex( final byte[] sequence, final int kmer ) { public DeBruijnVertex( final byte[] sequence, final int kmer ) {
this.sequence = sequence; this.sequence = sequence.clone();
this.kmer = kmer; this.kmer = kmer;
} }

2
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
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@ -42,7 +42,7 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP
protected RecalibrationTables recalibrationTables; protected RecalibrationTables recalibrationTables;
public void initialize(final Covariate[] covariates, final RecalibrationTables recalibrationTables) { public void initialize(final Covariate[] covariates, final RecalibrationTables recalibrationTables) {
this.covariates = covariates; this.covariates = covariates.clone();
this.recalibrationTables = recalibrationTables; this.recalibrationTables = recalibrationTables;
} }

14
public/java/src/org/broadinstitute/sting/utils/Haplotype.java
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@ -55,22 +55,22 @@ public class Haplotype {
* @param bases bases * @param bases bases
* @param qual qual * @param qual qual
*/ */
public Haplotype(byte[] bases, int qual) { public Haplotype( final byte[] bases, final int qual ) {
this.bases = bases; this.bases = bases.clone();
quals = new double[bases.length]; quals = new double[bases.length];
Arrays.fill(quals, (double)qual); Arrays.fill(quals, (double)qual);
} }
public Haplotype(byte[] bases, double[] quals) { public Haplotype( final byte[] bases, final double[] quals ) {
this.bases = bases; this.bases = bases.clone();
this.quals = quals; this.quals = quals.clone();
} }
public Haplotype(byte[] bases) { public Haplotype( final byte[] bases ) {
this(bases, 0); this(bases, 0);
} }
public Haplotype(byte[] bases, GenomeLoc loc) { public Haplotype( final byte[] bases, final GenomeLoc loc ) {
this(bases); this(bases);
this.genomeLocation = loc; this.genomeLocation = loc;
} }