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Re-enabling indels for the Genomic Annotator as per Steve's patch. Steve assures me that he will test this out really well. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4139 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-27 15:01:25 +00:00
parent 6f4af47aac
commit dda84a0e54
2 changed files with 41 additions and 43 deletions
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82
java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotation.java
View File

@ -122,58 +122,56 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
//The HAPLOTYPE_REFERENCE_COLUMN matches the variant's reference allele based on a case-insensitive string comparison. //The HAPLOTYPE_REFERENCE_COLUMN matches the variant's reference allele based on a case-insensitive string comparison.
//The HAPLOTYPE_ALTERNATE_COLUMN can optionally list more than allele separated by one of these chars: ,\/:| //The HAPLOTYPE_ALTERNATE_COLUMN can optionally list more than allele separated by one of these chars: ,\/:|
String hapAltValue = annotationsForRecord.get( generateInfoFieldKey(name, HAPLOTYPE_ALTERNATE_COLUMN) ); // only check this value for SNPs
if(hapAltValue != null) String hapAltValue = vc.isSNP() ? annotationsForRecord.get( generateInfoFieldKey(name, HAPLOTYPE_ALTERNATE_COLUMN) ) : null;
{ if ( hapAltValue != null && !hapAltValue.equals("*") ) {
if(!hapAltValue.equals("*")) Set<Allele> alternateAlleles = vc.getAlternateAlleles();
{ //if(alternateAlleles.isEmpty()) {
Set<Allele> alternateAlleles = vc.getAlternateAlleles(); //handle a site that has been called monomorphic reference
//if(alternateAlleles.isEmpty()) { //alternateAlleles.add(vc.getReference());
//handle a site that has been called monomorphic reference //continue; //TODO If this site is monomorphic in the VC, and the current record specifies a particular alternate allele, skip this record. Right?
//alternateAlleles.add(vc.getReference()); //} else
//continue; //TODO If this site is monomorphic in the VC, and the current record specifies a particular alternate allele, skip this record. Right? if(alternateAlleles.size() > 1) {
//} else throw new StingException("Record [" + vc + "] contains " + alternateAlleles.size() + " alternate alleles. GenomicAnnotion currently only supports annotating 1 alternate allele.");
if(alternateAlleles.size() > 1) { }
throw new StingException("Record [" + vc + "] contains " + alternateAlleles.size() + " alternate alleles. GenomicAnnotion currently only supports annotating 1 alternate allele.");
}
boolean positiveStrand = true; //if HAPLOTYPE_STRAND_COLUMN isn't specified, assume positive strand. boolean positiveStrand = true; //if HAPLOTYPE_STRAND_COLUMN isn't specified, assume positive strand.
String hapStrandValue = annotationsForRecord.get( generateInfoFieldKey(name, HAPLOTYPE_STRAND_COLUMN) ); String hapStrandValue = annotationsForRecord.get( generateInfoFieldKey(name, HAPLOTYPE_STRAND_COLUMN) );
if(hapStrandValue != null ) { if(hapStrandValue != null ) {
hapStrandValue = hapStrandValue.trim().toLowerCase(); hapStrandValue = hapStrandValue.trim().toLowerCase();
if(hapStrandValue.equals("-") || hapStrandValue.equals("r")) { if(hapStrandValue.equals("-") || hapStrandValue.equals("r")) {
positiveStrand = false; positiveStrand = false;
} else if(!hapStrandValue.equals("+") && !hapStrandValue.equals("f")) { } else if(!hapStrandValue.equals("+") && !hapStrandValue.equals("f")) {
throw new StingException("Record (" + gatkFeature.getUnderlyingObject() + ") in " + name + " has an invalid value for " + HAPLOTYPE_STRAND_COLUMN + ". This value is: \"" + hapStrandValue + "\""); throw new StingException("Record (" + gatkFeature.getUnderlyingObject() + ") in " + name + " has an invalid value for " + HAPLOTYPE_STRAND_COLUMN + ". This value is: \"" + hapStrandValue + "\"");
}
} }
}
Allele vcAlt; Allele vcAlt;
if(alternateAlleles.isEmpty()) { if(alternateAlleles.isEmpty()) {
vcAlt = vc.getReference(); vcAlt = vc.getReference();
} else { } else {
vcAlt = alternateAlleles.iterator().next(); vcAlt = alternateAlleles.iterator().next();
}
boolean matchFound = false;
for(String hapAlt : hapAltValue.split("[,\\\\/:|]")) {
if(!positiveStrand) {
hapAlt = new String(BaseUtils.simpleReverseComplement(hapAlt.getBytes()));
} }
boolean matchFound = false; if(!hapAlt.isEmpty() && vcAlt.basesMatch(hapAlt)) {
for(String hapAlt : hapAltValue.split("[,\\\\/:|]")) { matchFound = true;
if(!positiveStrand) { break;
hapAlt = new String(BaseUtils.simpleReverseComplement(hapAlt.getBytes()));
}
if(!hapAlt.isEmpty() && vcAlt.basesMatch(hapAlt)) {
matchFound = true;
break;
}
}
if(!matchFound) {
continue; //skip record - none of its alternate alleles match the variant's alternate allele
} }
} }
if(!matchFound) {
continue; //skip record - none of its alternate alleles match the variant's alternate allele
}
} }
String hapRefValue = annotationsForRecord.get( generateInfoFieldKey(name, HAPLOTYPE_REFERENCE_COLUMN) ); // only check this value for SNPs
String hapRefValue = vc.isSNP() ? annotationsForRecord.get( generateInfoFieldKey(name, HAPLOTYPE_REFERENCE_COLUMN) ) : null;
if(hapRefValue != null) if(hapRefValue != null)
{ {
hapRefValue = hapRefValue.trim(); hapRefValue = hapRefValue.trim();

2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/GenomicAnnotator.java
View File

@ -241,7 +241,7 @@ public class GenomicAnnotator extends RodWalker<Integer, Integer> implements Tre
Set<VariantContext> results = new LinkedHashSet<VariantContext>(); Set<VariantContext> results = new LinkedHashSet<VariantContext>();
for (VariantContext vc : tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false)) { for (VariantContext vc : tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false)) {
if ( vc.isFiltered() || if ( vc.isFiltered() ||
(vc.isVariant() && (!vc.isSNP() || !vc.isBiallelic())) ) { (vc.isVariant() && !vc.isBiallelic()) ) {
results.add(vc); results.add(vc);
} else { } else {
Map<String, StratifiedAlignmentContext> stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup()); Map<String, StratifiedAlignmentContext> stratifiedContexts = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup());