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Updated to use Tribble-based GATKFeature instead of TabularROD 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3388 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd 2010-05-19 03:40:47 +00:00
parent d65b2d32d1
commit d8469e2fba
1 changed files with 13 additions and 16 deletions
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29
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotation.java
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@ -13,9 +13,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele; import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.AnnotatorROD;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.TabularROD; import org.broadinstitute.sting.gatk.refdata.features.sampileup.AnnotatorInputTableFeature;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
@ -31,9 +30,10 @@ import org.broadinstitute.sting.utils.StingException;
*/ */
public class GenomicAnnotation implements InfoFieldAnnotation { public class GenomicAnnotation implements InfoFieldAnnotation {
private static final String HAPLOTYPE_REFERENCE_COLUMN = AnnotatorROD.HAPLOTYPE_REFERENCE_COLUMN; public static final String CHRPOS_COLUMN = "chrpos";
private static final String HAPLOTYPE_ALTERNATE_COLUMN = AnnotatorROD.HAPLOTYPE_ALTERNATE_COLUMN; public static final String HAPLOTYPE_REFERENCE_COLUMN = "haplotypeReference";
private static final String HAPLOTYPE_STRAND_COLUMN = AnnotatorROD.HAPLOTYPE_STRAND_COLUMN; public static final String HAPLOTYPE_ALTERNATE_COLUMN = "haplotypeAlternate";
public static final String HAPLOTYPE_STRAND_COLUMN = "haplotypeStrand";
/** /**
@ -72,18 +72,16 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
final Map<String, Object> annotations = new HashMap<String, Object>(); final Map<String, Object> annotations = new HashMap<String, Object>();
for(final GATKFeature gatkFeature : tracker.getAllRods()) for(final GATKFeature gatkFeature : tracker.getAllRods())
{ {
final Object rod = gatkFeature.getUnderlyingObject();
final String name = gatkFeature.getName(); final String name = gatkFeature.getName();
if( name.equals("variant") || name.equals("interval") ) { if( name.equals("variant") || name.equals("interval") ) {
continue; continue;
} }
if( ! (rod instanceof TabularROD) ) { if( ! (gatkFeature.getUnderlyingObject() instanceof AnnotatorInputTableFeature) ) {
continue; //GenericAnnotation only works with TabularRODs because it needs to be able to select individual columns. continue; //GenericAnnotation only works with TabularRODs because it needs to be able to select individual columns.
} }
TabularROD tabularRod = (TabularROD) rod; final Map<String, String> annotationsForRecord = convertRecordToAnnotations( gatkFeature );
final Map<String, String> annotationsForRecord = convertRecordToAnnotations( tabularRod );
//If this record contains the HAPLOTYPE_REFERENCE_COLUMN and/or HAPLOTYPE_ALTERNATE_COLUMN, check whether the //If this record contains the HAPLOTYPE_REFERENCE_COLUMN and/or HAPLOTYPE_ALTERNATE_COLUMN, check whether the
//alleles specified match the the variant's reference allele and alternate allele. //alleles specified match the the variant's reference allele and alternate allele.
@ -118,7 +116,7 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
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 (" + rod + ") 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 + "\"");
} }
} }
@ -183,18 +181,17 @@ public class GenomicAnnotation implements InfoFieldAnnotation {
* thisRodName.fieldName1=fieldValue, thisRodName.fieldName1=fieldValue * thisRodName.fieldName1=fieldValue, thisRodName.fieldName1=fieldValue
* (eg. dbSNP.avHet=0.7, dbSNP.ref_allele=A) * (eg. dbSNP.avHet=0.7, dbSNP.ref_allele=A)
* *
* @param rod A TabularROD corresponding to one record in one input file. * @param annotatorInputTableFeature AnnotatorInputTableFeature corresponding to one record in one input file.
* * @param name The binding name of the given AnnotatorInputTableFeature.
* @return The map of column-name -> value pairs. * @return The map of column-name -> value pairs.
*/ */
private Map<String, String> convertRecordToAnnotations( final TabularROD rod ) { private Map<String, String> convertRecordToAnnotations( final GATKFeature feature) {
final String rodName = rod.getName(); //aka the rod binding
final Map<String, String> result = new HashMap<String, String>(); final Map<String, String> result = new HashMap<String, String>();
for(final Entry<String, String> entry : rod.entrySet()) { for(final Entry<String, String> entry : ((AnnotatorInputTableFeature) feature.getUnderlyingObject()).getEntrySet()) {
final String value = entry.getValue(); final String value = entry.getValue();
if(!value.trim().isEmpty()) { if(!value.trim().isEmpty()) {
result.put( generateInfoFieldKey(rodName, entry.getKey()), entry.getValue()); result.put( generateInfoFieldKey(feature.getName(), entry.getKey()), entry.getValue());
} }
} }