diff --git a/java/src/org/broadinstitute/sting/utils/genotype/geli/GeliGenotypeCall.java b/java/src/org/broadinstitute/sting/utils/genotype/geli/GeliGenotypeCall.java index 327eabea5..d4422378f 100755 --- a/java/src/org/broadinstitute/sting/utils/genotype/geli/GeliGenotypeCall.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/geli/GeliGenotypeCall.java @@ -18,8 +18,8 @@ import java.util.Arrays; * The implementation of the genotype interface, specific to Geli */ public class GeliGenotypeCall implements Genotype, ReadBacked, PosteriorsBacked { - private char mRefBase; - private GenomeLoc mLocation; + private final char mRefBase; + private final GenomeLoc mLocation; private List mReads; private double[] mPosteriors; diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFGenotypeCall.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFGenotypeCall.java index 5a76d9f3b..8186d5a28 100755 --- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFGenotypeCall.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFGenotypeCall.java @@ -18,8 +18,8 @@ import java.util.Arrays; * The implementation of the genotype interface, specific to GLF */ public class GLFGenotypeCall implements Genotype, ReadBacked, LikelihoodsBacked { - private char mRefBase; - private GenomeLoc mLocation; + private final char mRefBase; + private final GenomeLoc mLocation; private List mReads; private double[] mLikelihoods; diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeCall.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeCall.java index 46b8ab7fc..0c6fc91fd 100755 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeCall.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeCall.java @@ -18,8 +18,8 @@ import java.util.List; * The implementation of the genotype interface, specific to VCF */ public class VCFGenotypeCall implements Genotype, ReadBacked, PosteriorsBacked, SampleBacked { - private char mRefBase; - private GenomeLoc mLocation; + private final char mRefBase; + private final GenomeLoc mLocation; private List mReads; private double[] mPosteriors; diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java index 18380a232..ac2213402 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java @@ -156,7 +156,7 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter { Map infoFields = getInfoFields(metadata, params); - double qual = (metadata == null) ? 0 : (metadata.getLOD()) * 10; + double qual = (metadata == null) ? 0 : metadata.getLOD(); // maintain 0-99 based Q-scores qual = Math.min(qual, 99); qual = Math.max(qual, 0);