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Always use phasing info when converting genotypes to strings 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3482 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-06-03 17:50:50 +00:00
parent e2b41082af
commit 597b3744ab
1 changed files with 25 additions and 21 deletions
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46
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/Genotype.java
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@ -10,6 +10,10 @@ import java.util.*;
* @author Mark DePristo * @author Mark DePristo
*/ */
public class Genotype { public class Genotype {
public final static String PHASED_ALLELE_SEPARATOR = "|";
public final static String UNPHASED_ALLELE_SEPARATOR = "/";
protected InferredGeneticContext commonInfo; protected InferredGeneticContext commonInfo;
public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR; public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR;
protected List<Allele> alleles = new ArrayList<Allele>(); protected List<Allele> alleles = new ArrayList<Allele>();
@ -50,20 +54,6 @@ public class Genotype {
return alleles.get(i); return alleles.get(i);
} }
private final static String ALLELE_SEPARATOR = "/";
public String getGenotypeString() {
return Utils.join(ALLELE_SEPARATOR, getAllelesString());
}
private List<String> getAllelesString() {
List<String> al = new ArrayList<String>();
for ( Allele a : alleles )
al.add(new String(a.getBases()));
return al;
}
public boolean genotypesArePhased() { return genotypesArePhased; } public boolean genotypesArePhased() { return genotypesArePhased; }
/** /**
@ -126,19 +116,33 @@ public class Genotype {
throw new IllegalArgumentException("BUG: alleles include some No Calls and some Calls, an illegal state " + this); throw new IllegalArgumentException("BUG: alleles include some No Calls and some Calls, an illegal state " + this);
} }
private String haplotypesString() { public String getGenotypeString() {
if ( genotypesArePhased() ) return getGenotypeString(true);
return Utils.join("|", getAlleles()); }
else
return Utils.join("/", Utils.sorted(getAlleles())); public String getGenotypeString(boolean ignoreRefState) {
// Notes:
// 1. Make sure to use the appropriate separator depending on whether the genotype is phased
// 2. If ignoreRefState is true, then we want just the bases of the Alleles (ignoring the '*' indicating a ref Allele)
// 3. So that everything is deterministic with regards to integration tests, we sort Alleles (when the genotype isn't phased, of course)
return Utils.join(genotypesArePhased() ? PHASED_ALLELE_SEPARATOR : UNPHASED_ALLELE_SEPARATOR,
ignoreRefState ? getAlleleStrings() : (genotypesArePhased() ? getAlleles() : Utils.sorted(getAlleles())));
}
private List<String> getAlleleStrings() {
List<String> al = new ArrayList<String>();
for ( Allele a : alleles )
al.add(new String(a.getBases()));
return al;
} }
public String toString() { public String toString() {
return String.format("[GT: %s %s %s Q%.2f %s]", getSampleName(), haplotypesString(), getType(), getPhredScaledQual(), Utils.sortedString(getAttributes())); return String.format("[GT: %s %s %s Q%.2f %s]", getSampleName(), getGenotypeString(false), getType(), getPhredScaledQual(), Utils.sortedString(getAttributes()));
} }
public String toBriefString() { public String toBriefString() {
return String.format("%s:Q%.2f", haplotypesString(), getPhredScaledQual()); return String.format("%s:Q%.2f", getGenotypeString(false), getPhredScaledQual());
} }
public boolean sameGenotype(Genotype other) { public boolean sameGenotype(Genotype other) {