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First attempt at implement record filtering based on special 'hap_ref', 'hap_alt' columns in the input files 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3118 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd 2010-04-02 21:52:26 +00:00
parent d78e7f6c0a
commit 705b28e90d
1 changed files with 46 additions and 7 deletions
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53
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotation.java
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@ -10,19 +10,27 @@ import java.util.Map.Entry;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.TabularROD;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.genotype.vcf.VCFInfoHeaderLine;
/**
* TODO comment
*/
public class GenomicAnnotation implements InfoFieldAnnotation {
private static final String HAP_REF = "hap_ref";
private static final String HAP_ALT = "hap_alt";
/**
* For each ROD (aka. record) which overlaps the current locus, generates a
@ -54,19 +62,50 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
for(final GATKFeature gatkFeature : tracker.getAllRods())
{
final ReferenceOrderedDatum rod = (ReferenceOrderedDatum) gatkFeature.getUnderlyingObject();
if(! (rod instanceof TabularROD) ) {
continue; //GenericAnnotation only works with TabularRODs so that it can select individual columns
}
final String name = rod.getName();
if(name.equals("variant") || name.equals("interval")) {
if( name.equals("variant") || name.equals("interval") ) {
continue;
}
if( ! (rod instanceof TabularROD) ) {
continue; //GenericAnnotation only works with TabularRODs so that it can select individual columns
}
final Map<String, String> annotationsForRecord = convertRecordToAnnotations( (TabularROD) rod );
TabularROD tabularRod = (TabularROD) rod;
final Map<String, String> annotationsForRecord = convertRecordToAnnotations( tabularRod );
List<Map<String, String>> listOfMatchingRecords = (List<Map<String, String>>) annotations.get(name);
//filter by matching the vc's reference allele and alternate allele to the record's HAP_REF and HAP_ALT columns.
final String hapAltValue = annotationsForRecord.get( generateInfoFieldKey(name, HAP_ALT) );
if(hapAltValue != null && !hapAltValue.equals("*")) {
Set<Allele> alternateAlleles = vc.getAlternateAlleles();
if(alternateAlleles.isEmpty()) {
//TODO If this site is monomorphic in the VC, and the current record specifies a particular alternate allele, skip this record. Right?
continue;
} else if(alternateAlleles.size() > 1) {
throw new StingException("Record (" + rod + ") in " + name + " contains " + alternateAlleles.size() + " alternate alleles. GenomicAnnotion currently only supports annotating 1 alternate allele.");
}
//TODO handle strand somehow?
//decide whether to skip this record.
Allele vcAlt = alternateAlleles.iterator().next();
if(!vcAlt.basesMatch(hapAltValue)) {
//TODO check the intersection of vcAlt and hapAltValue
continue; //skip record
}
}
final String hapRefValue = annotationsForRecord.get( generateInfoFieldKey(name, HAP_REF) );
if(hapRefValue != null && !hapRefValue.equals("*")) {
//match against hapRef
Allele vcRef = vc.getReference();
if(!vcRef.basesMatch(hapRefValue)) {
//TODO check the intersection of vcRef and hapRefValue
continue; //skip record
}
}
List<Map<String, String>> listOfMatchingRecords = (List<Map<String, String>>) annotations.get( name );
if(listOfMatchingRecords == null) {
listOfMatchingRecords = new LinkedList<Map<String,String>>();
listOfMatchingRecords.add( annotationsForRecord );