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Moved removePLs to VariantContextUtils

This commit is contained in:
Mark DePristo 2011-09-23 08:23:46 -04:00
parent 054c475416
commit 4397ce8653
2 changed files with 8 additions and 8 deletions
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7
public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
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@ -74,13 +74,6 @@ public class Genotype {
return new Genotype(g.getSampleName(), g.getAlleles(), g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, attributes, g.isPhased()); return new Genotype(g.getSampleName(), g.getAlleles(), g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, attributes, g.isPhased());
} }
public static Genotype removePLs(Genotype g) {
Map<String, Object> attrs = new HashMap<String, Object>(g.getAttributes());
attrs.remove(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY);
attrs.remove(VCFConstants.GENOTYPE_LIKELIHOODS_KEY);
return new Genotype(g.getSampleName(), g.getAlleles(), g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, attrs, g.isPhased());
}
public static Genotype modifyAlleles(Genotype g, List<Allele> alleles) { public static Genotype modifyAlleles(Genotype g, List<Allele> alleles) {
return new Genotype(g.getSampleName(), alleles, g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, g.getAttributes(), g.isPhased()); return new Genotype(g.getSampleName(), alleles, g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, g.getAttributes(), g.isPhased());
} }

9
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -159,6 +159,13 @@ public class VariantContextUtils {
return "%." + precision + "f"; return "%." + precision + "f";
} }
public static Genotype removePLs(Genotype g) {
Map<String, Object> attrs = new HashMap<String, Object>(g.getAttributes());
attrs.remove(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY);
attrs.remove(VCFConstants.GENOTYPE_LIKELIHOODS_KEY);
return new Genotype(g.getSampleName(), g.getAlleles(), g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, attrs, g.isPhased());
}
/** /**
* A simple but common wrapper for matching VariantContext objects using JEXL expressions * A simple but common wrapper for matching VariantContext objects using JEXL expressions
*/ */
@ -740,7 +747,7 @@ public class VariantContextUtils {
Map<String, Genotype> newGs = new HashMap<String, Genotype>(genotypes.size()); Map<String, Genotype> newGs = new HashMap<String, Genotype>(genotypes.size());
for ( Map.Entry<String, Genotype> g : genotypes.entrySet() ) { for ( Map.Entry<String, Genotype> g : genotypes.entrySet() ) {
newGs.put(g.getKey(), g.getValue().hasLikelihoods() ? Genotype.removePLs(g.getValue()) : g.getValue()); newGs.put(g.getKey(), g.getValue().hasLikelihoods() ? removePLs(g.getValue()) : g.getValue());
} }
return newGs; return newGs;