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-Mark just reminded me: actually force the ref/loc to be immutable 

-VCF writer should be blind to the score/confidence/lod value - just print the thing out as is


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1932 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-10-29 13:41:53 +00:00
parent 5cdbdd9e5b
commit 1c4ca9d383
4 changed files with 7 additions and 7 deletions
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4
java/src/org/broadinstitute/sting/utils/genotype/geli/GeliGenotypeCall.java
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@ -18,8 +18,8 @@ import java.util.Arrays;
* The implementation of the genotype interface, specific to Geli * The implementation of the genotype interface, specific to Geli
*/ */
public class GeliGenotypeCall implements Genotype, ReadBacked, PosteriorsBacked { public class GeliGenotypeCall implements Genotype, ReadBacked, PosteriorsBacked {
private char mRefBase; private final char mRefBase;
private GenomeLoc mLocation; private final GenomeLoc mLocation;
private List<SAMRecord> mReads; private List<SAMRecord> mReads;
private double[] mPosteriors; private double[] mPosteriors;

4
java/src/org/broadinstitute/sting/utils/genotype/glf/GLFGenotypeCall.java
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@ -18,8 +18,8 @@ import java.util.Arrays;
* The implementation of the genotype interface, specific to GLF * The implementation of the genotype interface, specific to GLF
*/ */
public class GLFGenotypeCall implements Genotype, ReadBacked, LikelihoodsBacked { public class GLFGenotypeCall implements Genotype, ReadBacked, LikelihoodsBacked {
private char mRefBase; private final char mRefBase;
private GenomeLoc mLocation; private final GenomeLoc mLocation;
private List<SAMRecord> mReads; private List<SAMRecord> mReads;
private double[] mLikelihoods; private double[] mLikelihoods;

4
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeCall.java
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@ -18,8 +18,8 @@ import java.util.List;
* The implementation of the genotype interface, specific to VCF * The implementation of the genotype interface, specific to VCF
*/ */
public class VCFGenotypeCall implements Genotype, ReadBacked, PosteriorsBacked, SampleBacked { public class VCFGenotypeCall implements Genotype, ReadBacked, PosteriorsBacked, SampleBacked {
private char mRefBase; private final char mRefBase;
private GenomeLoc mLocation; private final GenomeLoc mLocation;
private List<SAMRecord> mReads; private List<SAMRecord> mReads;
private double[] mPosteriors; private double[] mPosteriors;

2
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
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@ -156,7 +156,7 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
Map<String, String> infoFields = getInfoFields(metadata, params); Map<String, String> 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 // maintain 0-99 based Q-scores
qual = Math.min(qual, 99); qual = Math.min(qual, 99);
qual = Math.max(qual, 0); qual = Math.max(qual, 0);