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Fix for Kiran: -1 is a valid value for genotype qualities in VCF, so VariantContext shouldn't die. Cleaned up the relevant VCF code while I was in there. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3015 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-17 00:20:15 +00:00
parent 849bd1f451
commit 1fd909cdaf
3 changed files with 25 additions and 7 deletions
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5
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -193,11 +193,12 @@ public class VariantContextAdaptors {
if ( vcfG.isFiltered() ) // setup the FL genotype filter fields if ( vcfG.isFiltered() ) // setup the FL genotype filter fields
genotypeFilters.addAll(Arrays.asList(vcfG.getFields().get(VCFGenotypeRecord.GENOTYPE_FILTER_KEY).split(";"))); genotypeFilters.addAll(Arrays.asList(vcfG.getFields().get(VCFGenotypeRecord.GENOTYPE_FILTER_KEY).split(";")));
Genotype g = new Genotype(vcfG.getSampleName(), genotypeAlleles, vcfG.getNegLog10PError(), genotypeFilters, fields, vcfG.getPhaseType() == VCFGenotypeRecord.PHASE.PHASED); double qual = vcfG.isMissingQual() ? VariantContext.NO_NEG_LOG_10PERROR : vcfG.getNegLog10PError();
Genotype g = new Genotype(vcfG.getSampleName(), genotypeAlleles, qual, genotypeFilters, fields, vcfG.getPhaseType() == VCFGenotypeRecord.PHASE.PHASED);
genotypes.put(g.getSampleName(), g); genotypes.put(g.getSampleName(), g);
} }
double qual = vcf.getQual() == -1 ? VariantContext.NO_NEG_LOG_10PERROR : vcf.getNegLog10PError(); double qual = vcf.isMissingQual() ? VariantContext.NO_NEG_LOG_10PERROR : vcf.getNegLog10PError();
VariantContext vc = new VariantContext(name, vcf.getLocation(), alleles, genotypes, qual, filters, attributes); VariantContext vc = new VariantContext(name, vcf.getLocation(), alleles, genotypes, qual, filters, attributes);
vc.validate(); vc.validate();
return vc; return vc;

14
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java
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@ -127,8 +127,20 @@ public class VCFGenotypeRecord {
return mFields; return mFields;
} }
/**
* @return the phred-scaled quality score
*/
public double getQual() {
return ( mFields.containsKey(GENOTYPE_QUALITY_KEY) ? Double.valueOf(mFields.get(GENOTYPE_QUALITY_KEY)) : MISSING_GENOTYPE_QUALITY);
}
public boolean isMissingQual() {
return (int)getQual() == MISSING_GENOTYPE_QUALITY;
}
public double getNegLog10PError() { public double getNegLog10PError() {
return ( mFields.containsKey(GENOTYPE_QUALITY_KEY) ? Double.valueOf(mFields.get(GENOTYPE_QUALITY_KEY)) / 10.0 : MISSING_GENOTYPE_QUALITY); double qual = getQual();
return (qual == MISSING_GENOTYPE_QUALITY ? MISSING_GENOTYPE_QUALITY : qual / 10.0);
} }
public int getReadCount() { public int getReadCount() {

13
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
View File

@ -39,6 +39,7 @@ public class VCFRecord {
public static final String EMPTY_ID_FIELD = "."; public static final String EMPTY_ID_FIELD = ".";
public static final String EMPTY_ALLELE_FIELD = "."; public static final String EMPTY_ALLELE_FIELD = ".";
public static final String DOUBLE_PRECISION_FORMAT_STRING = "%.2f"; public static final String DOUBLE_PRECISION_FORMAT_STRING = "%.2f";
public static final int MISSING_GENOTYPE_QUALITY = -1;
// the reference base // the reference base
private String mReferenceBases; private String mReferenceBases;
@ -350,6 +351,10 @@ public class VCFRecord {
return mQual; return mQual;
} }
public boolean isMissingQual() {
return (int)mQual == MISSING_GENOTYPE_QUALITY;
}
/** /**
* @return the -log10PError * @return the -log10PError
*/ */
@ -448,8 +453,8 @@ public class VCFRecord {
} }
public void setQual(double qual) { public void setQual(double qual) {
if ( qual < 0 && MathUtils.compareDoubles(qual, -1.0) != 0 ) if ( qual < 0 && (int)qual != MISSING_GENOTYPE_QUALITY )
throw new IllegalArgumentException("Qual values cannot be negative unless they are -1 ('unknown')"); throw new IllegalArgumentException("Qual values cannot be negative unless they are " + MISSING_GENOTYPE_QUALITY + " ('unknown')");
mQual = qual; mQual = qual;
} }
@ -555,8 +560,8 @@ public class VCFRecord {
builder.append(EMPTY_ALLELE_FIELD); builder.append(EMPTY_ALLELE_FIELD);
} }
builder.append(FIELD_SEPERATOR); builder.append(FIELD_SEPERATOR);
if ( MathUtils.compareDoubles(mQual, -1.0) == 0 ) if ( (int)mQual == MISSING_GENOTYPE_QUALITY )
builder.append("-1"); builder.append(MISSING_GENOTYPE_QUALITY);
else else
builder.append(String.format(DOUBLE_PRECISION_FORMAT_STRING, mQual)); builder.append(String.format(DOUBLE_PRECISION_FORMAT_STRING, mQual));
builder.append(FIELD_SEPERATOR); builder.append(FIELD_SEPERATOR);