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Fixed ValidatingPileup to work with Andrey's new rodSAMPileup -> GenotypeList type hierarchy. 

Fixed reference-ordered data validation system to validate class hierarchies instead of specific class types.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@811 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-05-23 20:50:28 +00:00
parent d056f9f3e8
commit 008d677bea
2 changed files with 21 additions and 4 deletions
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7
java/src/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedData.java
View File

@ -140,14 +140,15 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
public String getName() { return name; }
/**
* Special equals override to see if this ROD is of type name, type.
* Implemented to preserve data hiding whenever possible.
* Special equals override to see if this ROD is compatible with the given
* name and type. 'Compatible' means that this ROD has the name that's passed
* in and its data can fit into the container specified by type.
* @param name Name to check.
* @param type Type to check.
* @return True if these parameters imply this rod. False otherwise.
*/
public boolean matches( String name, Class<? extends ReferenceOrderedDatum> type ) {
return this.name.equals(name) && this.type.equals(type);
return this.name.equals(name) && type.isAssignableFrom(this.type);
}
public RODIterator iterator() {

18
java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java
View File

@ -24,7 +24,7 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
Pileup pileup = new ReadBackedPileup(ref, context);
Pileup truePileup = (Pileup)tracker.lookup("pileup", null);
Pileup truePileup = getTruePileup( tracker );
if ( truePileup == null ) {
System.out.printf("No truth pileup data available at %s%n", pileup.getPileupString());
@ -59,6 +59,22 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
combined.nBases = lhs.nBases + rhs.nBases;
return combined;
}
/**
* Extracts the true pileup data from the given rodSAMPileup. Note that this implementation
* assumes that the genotype will only be point or indel.
* @param tracker ROD tracker from which to extract pileup data.
* @return True pileup data.
*/
private Pileup getTruePileup( RefMetaDataTracker tracker ) {
rodSAMPileup pileup = (rodSAMPileup)tracker.lookup("pileup", null);
if( pileup.hasPointGenotype() )
return (Pileup)pileup.getPointGenotype();
else if( pileup.hasIndelGenotype() )
return (Pileup)pileup.getIndelGenotype();
else
throw new StingException("Unsupported pileup type: " + pileup);
}
}
class ValidationStats {