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ID field now stored in the VariantContext itself, not the attributes

This commit is contained in:
Mark DePristo 2011-11-15 14:56:33 -05:00
parent 233e581828
commit 460a51f473
22 changed files with 182 additions and 196 deletions
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14
public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
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@ -6,8 +6,10 @@ import org.broad.tribble.annotation.Strand;
import org.broad.tribble.dbsnp.OldDbSNPFeature;
import org.broad.tribble.gelitext.GeliTextFeature;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
import org.broadinstitute.sting.utils.variantcontext.*;
@ -187,7 +189,6 @@ public class VariantContextAdaptors {
}
Map<String, Object> attributes = new HashMap<String, Object>();
attributes.put(VariantContext.ID_KEY, dbsnp.getRsID());
int index = dbsnp.getStart() - ref.getWindow().getStart() - 1;
if ( index < 0 )
@ -195,7 +196,7 @@ public class VariantContextAdaptors {
Byte refBaseForIndel = new Byte(ref.getBases()[index]);
GenotypeCollection genotypes = null;
VariantContext vc = new VariantContext(name, dbsnp.getChr(), dbsnp.getStart() - (sawNullAllele ? 1 : 0), dbsnp.getEnd() - (refAllele.isNull() ? 1 : 0), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes, refBaseForIndel);
VariantContext vc = new VariantContext(name, dbsnp.getRsID(), dbsnp.getChr(), dbsnp.getStart() - (sawNullAllele ? 1 : 0), dbsnp.getEnd() - (refAllele.isNull() ? 1 : 0), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes, refBaseForIndel);
return vc;
} else
return null; // can't handle anything else
@ -255,8 +256,8 @@ public class VariantContextAdaptors {
// add the call to the genotype list, and then use this list to create a VariantContext
genotypes.add(call);
alleles.add(refAllele);
VariantContext vc = VariantContextUtils.toVC(name, ref.getGenomeLocParser().createGenomeLoc(geli.getChr(),geli.getStart()), alleles, genotypes, geli.getLODBestToReference(), null, attributes);
return vc;
GenomeLoc loc = ref.getGenomeLocParser().createGenomeLoc(geli.getChr(),geli.getStart());
return new VariantContext(name, VCFConstants.EMPTY_ID_FIELD, loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, geli.getLODBestToReference(), null, attributes);
} else
return null; // can't handle anything else
}
@ -347,13 +348,10 @@ public class VariantContextAdaptors {
genotypes.add(g);
}
HashMap<String, Object> attrs = new HashMap<String, Object>(1);
attrs.put(VariantContext.ID_KEY, hapmap.getName());
long end = hapmap.getEnd();
if ( deletionLength > 0 )
end += deletionLength;
VariantContext vc = new VariantContext(name, hapmap.getChr(), hapmap.getStart(), end, alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attrs, refBaseForIndel);
VariantContext vc = new VariantContext(name, hapmap.getName(), hapmap.getChr(), hapmap.getStart(), end, alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, null, refBaseForIndel);
return vc;
}
}

11
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
View File

@ -163,11 +163,10 @@ public class VariantAnnotatorEngine {
}
public VariantContext annotateContext(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
Map<String, Object> infoAnnotations = new LinkedHashMap<String, Object>(vc.getAttributes());
// annotate db occurrences
annotateDBs(tracker, ref, vc, infoAnnotations);
vc = annotateDBs(tracker, ref, vc, infoAnnotations);
// annotate expressions where available
annotateExpressions(tracker, ref, infoAnnotations);
@ -186,14 +185,14 @@ public class VariantAnnotatorEngine {
return VariantContext.modifyGenotypes(annotatedVC, annotateGenotypes(tracker, ref, stratifiedContexts, vc));
}
private void annotateDBs(RefMetaDataTracker tracker, ReferenceContext ref, VariantContext vc, Map<String, Object> infoAnnotations) {
private VariantContext annotateDBs(RefMetaDataTracker tracker, ReferenceContext ref, VariantContext vc, Map<String, Object> infoAnnotations) {
for ( Map.Entry<RodBinding<VariantContext>, String> dbSet : dbAnnotations.entrySet() ) {
if ( dbSet.getValue().equals(VCFConstants.DBSNP_KEY) ) {
String rsID = VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbSet.getKey(), ref.getLocus()), vc.getType());
infoAnnotations.put(VCFConstants.DBSNP_KEY, rsID != null);
// annotate dbsnp id if available and not already there
if ( rsID != null && (!vc.hasID() || vc.getID().equals(VCFConstants.EMPTY_ID_FIELD)) )
infoAnnotations.put(VariantContext.ID_KEY, rsID);
if ( rsID != null && vc.emptyID() )
vc = VariantContext.modifyID(vc, rsID);
} else {
boolean overlapsComp = false;
for ( VariantContext comp : tracker.getValues(dbSet.getKey(), ref.getLocus()) ) {
@ -205,6 +204,8 @@ public class VariantAnnotatorEngine {
infoAnnotations.put(dbSet.getValue(), overlapsComp);
}
}
return vc;
}
private void annotateExpressions(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, Object> infoAnnotations) {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
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@ -333,11 +333,11 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
VariantContext filteredVC;
if ( beagleVarCounts > 0 || DONT_FILTER_MONOMORPHIC_SITES )
filteredVC = new VariantContext("outputvcf", vc_input.getChr(), vc_input.getStart(), vc_input.getEnd(), vc_input.getAlleles(), genotypes, vc_input.getNegLog10PError(), vc_input.filtersWereApplied() ? vc_input.getFilters() : null, vc_input.getAttributes());
filteredVC = new VariantContext("outputvcf", VCFConstants.EMPTY_ID_FIELD, vc_input.getChr(), vc_input.getStart(), vc_input.getEnd(), vc_input.getAlleles(), genotypes, vc_input.getNegLog10PError(), vc_input.filtersWereApplied() ? vc_input.getFilters() : null, vc_input.getAttributes());
else {
Set<String> removedFilters = vc_input.filtersWereApplied() ? new HashSet<String>(vc_input.getFilters()) : new HashSet<String>(1);
removedFilters.add(String.format("BGL_RM_WAS_%s",vc_input.getAlternateAllele(0)));
filteredVC = new VariantContext("outputvcf", vc_input.getChr(), vc_input.getStart(), vc_input.getEnd(), new HashSet<Allele>(Arrays.asList(vc_input.getReference())), genotypes, vc_input.getNegLog10PError(), removedFilters, vc_input.getAttributes());
filteredVC = new VariantContext("outputvcf", VCFConstants.EMPTY_ID_FIELD, vc_input.getChr(), vc_input.getStart(), vc_input.getEnd(), new HashSet<Allele>(Arrays.asList(vc_input.getReference())), genotypes, vc_input.getNegLog10PError(), removedFilters, vc_input.getAttributes());
}
HashMap<String, Object> attributes = new HashMap<String, Object>(filteredVC.getAttributes());

4
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
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@ -90,7 +90,7 @@ public class VCFDiffableReader implements DiffableReader {
// add fields
vcRoot.add("CHROM", vc.getChr());
vcRoot.add("POS", vc.getStart());
vcRoot.add("ID", vc.hasID() ? vc.getID() : VCFConstants.MISSING_VALUE_v4);
vcRoot.add("ID", vc.getID());
vcRoot.add("REF", vc.getReference());
vcRoot.add("ALT", vc.getAlternateAlleles());
vcRoot.add("QUAL", vc.hasNegLog10PError() ? vc.getNegLog10PError() * 10 : VCFConstants.MISSING_VALUE_v4);
@ -98,7 +98,7 @@ public class VCFDiffableReader implements DiffableReader {
// add info fields
for (Map.Entry<String, Object> attribute : vc.getAttributes().entrySet()) {
if ( ! attribute.getKey().startsWith("_") && ! attribute.getKey().equals(VariantContext.ID_KEY))
if ( ! attribute.getKey().startsWith("_") )
vcRoot.add(attribute.getKey(), attribute.getValue());
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -327,7 +327,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
if ( genotypes == null )
filteredVC = VariantContext.modifyFilters(vc, filters);
else
filteredVC = new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), filters, vc.getAttributes());
filteredVC = new VariantContext(vc.getSource(), vc.getID(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), filters, vc.getAttributes());
writer.add(filteredVC);
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
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@ -140,7 +140,7 @@ public class UGCallVariants extends RodWalker<VariantCallContext, Integer> {
VariantContext vc = VCs.get(0);
throw new UserException("There is no ALT allele in any of the VCF records passed in at " + vc.getChr() + ":" + vc.getStart());
}
return new VariantContext("VCwithGLs", variantVC.getChr(), variantVC.getStart(), variantVC.getEnd(), variantVC.getAlleles(), genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, null);
return new VariantContext("VCwithGLs", VCFConstants.EMPTY_ID_FIELD, variantVC.getChr(), variantVC.getStart(), variantVC.getEnd(), variantVC.getAlleles(), genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, null);
}
private static GenotypeCollection getGenotypesWithGLs(GenotypeCollection genotypes) {

10
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -229,7 +229,7 @@ public class UnifiedGenotyperEngine {
VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, rawContext.getLocation(), false, logger, UAC.alleles);
if ( vcInput == null )
return null;
vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles(), VariantContext.NO_NEG_LOG_10PERROR, null, null, ref.getBase());
vc = new VariantContext("UG_call", VCFConstants.EMPTY_ID_FIELD, vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles(), VariantContext.NO_NEG_LOG_10PERROR, null, null, ref.getBase());
} else {
// deal with bad/non-standard reference bases
@ -238,7 +238,7 @@ public class UnifiedGenotyperEngine {
Set<Allele> alleles = new HashSet<Allele>();
alleles.add(Allele.create(ref.getBase(), true));
vc = new VariantContext("UG_call", ref.getLocus().getContig(), ref.getLocus().getStart(), ref.getLocus().getStart(), alleles);
vc = new VariantContext("UG_call", VCFConstants.EMPTY_ID_FIELD, ref.getLocus().getContig(), ref.getLocus().getStart(), ref.getLocus().getStart(), alleles);
}
if ( annotationEngine != null ) {
@ -288,7 +288,7 @@ public class UnifiedGenotyperEngine {
int endLoc = calculateEndPos(alleles, refAllele, loc);
return new VariantContext("UG_call",
loc.getContig(),
VCFConstants.EMPTY_ID_FIELD, loc.getContig(),
loc.getStart(),
endLoc,
alleles,
@ -420,7 +420,7 @@ public class UnifiedGenotyperEngine {
myAlleles = new HashSet<Allele>(1);
myAlleles.add(vc.getReference());
}
VariantContext vcCall = new VariantContext("UG_call", loc.getContig(), loc.getStart(), endLoc,
VariantContext vcCall = new VariantContext("UG_call", VCFConstants.EMPTY_ID_FIELD, loc.getContig(), loc.getStart(), endLoc,
myAlleles, genotypes, phredScaledConfidence/10.0, passesCallThreshold(phredScaledConfidence) ? null : filter, attributes, refContext.getBase());
if ( annotationEngine != null ) {
@ -504,7 +504,7 @@ public class UnifiedGenotyperEngine {
myAlleles = new HashSet<Allele>(1);
myAlleles.add(vc.getReference());
}
VariantContext vcCall = new VariantContext("UG_call", loc.getContig(), loc.getStart(), endLoc,
VariantContext vcCall = new VariantContext("UG_call", VCFConstants.EMPTY_ID_FIELD, loc.getContig(), loc.getStart(), endLoc,
myAlleles, genotypes, phredScaledConfidence/10.0, passesCallThreshold(phredScaledConfidence) ? null : filter, attributes, vc.getReferenceBaseForIndel());
return new VariantCallContext(vcCall, confidentlyCalled(phredScaledConfidence, PofF));

4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
View File

@ -1074,7 +1074,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
filters = new HashSet<String>();
filters.add("NoCall");
}
VariantContext vc = new VariantContext("IGv2_Indel_call", refName, start, stop, alleles, genotypes,
VariantContext vc = new VariantContext("IGv2_Indel_call", VCFConstants.EMPTY_ID_FIELD, refName, start, stop, alleles, genotypes,
-1.0 /* log error */, filters, null, refBases[(int)start-1]);
vcf.add(vc);
}
@ -1171,7 +1171,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
filters.add("TCov");
}
VariantContext vc = new VariantContext("IGv2_Indel_call", refName, start, stop, alleles, genotypes,
VariantContext vc = new VariantContext("IGv2_Indel_call", VCFConstants.EMPTY_ID_FIELD, refName, start, stop, alleles, genotypes,
-1.0 /* log error */, filters, attrs, refBases[(int)start-1]);
vcf.add(vc);
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -1141,7 +1141,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
}
public VariantContext toVariantContext() {
return new VariantContext(name, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes);
return new VariantContext(name, VCFConstants.EMPTY_ID_FIELD, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes);
}
public GenomeLoc getLocation() {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
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@ -223,6 +223,6 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
newGenotypes.add(Genotype.modifyAlleles(genotype, newAlleles));
}
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), alleleMap.values(), newGenotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes(), refBaseForIndel);
return new VariantContext(vc.getSource(), vc.getID(), vc.getChr(), vc.getStart(), vc.getEnd(), alleleMap.values(), newGenotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes(), refBaseForIndel);
}
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
View File

@ -315,7 +315,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
getters.put("FILTER", new Getter() { public String get(VariantContext vc) {
return vc.isNotFiltered() ? "PASS" : Utils.join(",", vc.getFilters()); }
});
getters.put("ID", new Getter() { public String get(VariantContext vc) { return vc.hasID() ? vc.getID() : "."; } });
getters.put("ID", new Getter() { public String get(VariantContext vc) { return vc.getID(); } });
getters.put("HET", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHetCount()); } });
getters.put("HOM-REF", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomRefCount()); } });
getters.put("HOM-VAR", new Getter() { public String get(VariantContext vc) { return Integer.toString(vc.getHomVarCount()); } });

8
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
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@ -121,10 +121,8 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
Collection<VariantContext> contexts = getVariantContexts(tracker, ref);
for ( VariantContext vc : contexts ) {
Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
if ( rsID != null && !vc.hasID() ) {
attrs.put(VariantContext.ID_KEY, rsID);
vc = VariantContext.modifyAttributes(vc, attrs);
if ( rsID != null && vc.emptyID() ) {
vc = VariantContext.modifyID(vc, rsID);
}
// set the appropriate sample name if necessary
@ -203,7 +201,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
while ( dbsnpIterator.hasNext() ) {
GATKFeature feature = dbsnpIterator.next();
VariantContext vc = (VariantContext)feature.getUnderlyingObject();
if ( vc.hasID() && vc.getID().equals(rsID) )
if ( vc.getID().equals(rsID) )
return vc;
}

11
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -264,7 +264,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
else if ( parts[2].equals(VCFConstants.EMPTY_ID_FIELD) )
id = VCFConstants.EMPTY_ID_FIELD;
else
id = new String(parts[2]);
id = parts[2];
String ref = getCachedString(parts[3].toUpperCase());
String alts = getCachedString(parts[4].toUpperCase());
Double qual = parseQual(parts[5]);
@ -274,7 +274,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
// get our alleles, filters, and setup an attribute map
List<Allele> alleles = parseAlleles(ref, alts, lineNo);
Set<String> filters = parseFilters(filter);
Map<String, Object> attributes = parseInfo(info, id);
Map<String, Object> attributes = parseInfo(info);
// find out our current location, and clip the alleles down to their minimum length
int loc = pos;
@ -295,7 +295,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
VariantContext vc = null;
try {
vc = new VariantContext(name, contig, pos, loc, alleles, qual, filters, attributes, ref.getBytes()[0]);
vc = new VariantContext(name, id, contig, pos, loc, alleles, qual, filters, attributes, ref.getBytes()[0]);
} catch (Exception e) {
generateException(e.getMessage());
}
@ -349,10 +349,9 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
/**
* parse out the info fields
* @param infoField the fields
* @param id the indentifier
* @return a mapping of keys to objects
*/
private Map<String, Object> parseInfo(String infoField, String id) {
private Map<String, Object> parseInfo(String infoField) {
Map<String, Object> attributes = new HashMap<String, Object>();
if ( infoField.length() == 0 )
@ -391,8 +390,6 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
}
}
if ( ! id.equals(VCFConstants.EMPTY_ID_FIELD) )
attributes.put(VariantContext.ID_KEY, id);
return attributes;
}

4
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
View File

@ -182,7 +182,7 @@ public class StandardVCFWriter extends IndexingVCFWriter {
mWriter.write(VCFConstants.FIELD_SEPARATOR);
// ID
String ID = vc.hasID() ? vc.getID() : VCFConstants.EMPTY_ID_FIELD;
String ID = vc.getID();
mWriter.write(ID);
mWriter.write(VCFConstants.FIELD_SEPARATOR);
@ -227,7 +227,7 @@ public class StandardVCFWriter extends IndexingVCFWriter {
Map<String, String> infoFields = new TreeMap<String, String>();
for ( Map.Entry<String, Object> field : vc.getAttributes().entrySet() ) {
String key = field.getKey();
if ( key.equals(VariantContext.ID_KEY) || key.equals(VariantContext.UNPARSED_GENOTYPE_MAP_KEY) || key.equals(VariantContext.UNPARSED_GENOTYPE_PARSER_KEY) )
if ( key.equals(VariantContext.UNPARSED_GENOTYPE_MAP_KEY) || key.equals(VariantContext.UNPARSED_GENOTYPE_PARSER_KEY) )
continue;
String outputValue = formatVCFField(field.getValue());

5
public/java/src/org/broadinstitute/sting/utils/gcf/GCF.java
View File

@ -25,6 +25,7 @@
package org.broadinstitute.sting.utils.gcf;
import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
@ -148,7 +149,7 @@ public class GCF {
Byte refPadByte = refPad == 0 ? null : refPad;
GenotypeCollection genotypes = decodeGenotypes(header);
return new VariantContext(source, contig, start, stop, alleleMap, genotypes, negLog10PError, filters, attributes, refPadByte);
return new VariantContext(source, VCFConstants.EMPTY_ID_FIELD, contig, start, stop, alleleMap, genotypes, negLog10PError, filters, attributes, refPadByte);
}
private GenotypeCollection decodeGenotypes(final GCFHeader header) {
@ -193,7 +194,7 @@ public class GCF {
boolean first = true;
for ( Map.Entry<String, Object> field : vc.getAttributes().entrySet() ) {
String key = field.getKey();
if ( key.equals(VariantContext.ID_KEY) || key.equals(VariantContext.UNPARSED_GENOTYPE_MAP_KEY) || key.equals(VariantContext.UNPARSED_GENOTYPE_PARSER_KEY) )
if ( key.equals(VariantContext.UNPARSED_GENOTYPE_MAP_KEY) || key.equals(VariantContext.UNPARSED_GENOTYPE_PARSER_KEY) )
continue;
int stringIndex = GCFHeaderBuilder.encodeString(key);
String outputValue = StandardVCFWriter.formatVCFField(field.getValue());

109
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
View File

@ -167,16 +167,19 @@ public class VariantContext implements Feature { // to enable tribble intergrati
public final static double NO_NEG_LOG_10PERROR = CommonInfo.NO_NEG_LOG_10PERROR;
public final static String UNPARSED_GENOTYPE_MAP_KEY = "_UNPARSED_GENOTYPE_MAP_";
public final static String UNPARSED_GENOTYPE_PARSER_KEY = "_UNPARSED_GENOTYPE_PARSER_";
public final static String ID_KEY = "ID";
@Deprecated // ID is no longer stored in the attributes map
private final static String ID_KEY = "ID";
private final Byte REFERENCE_BASE_FOR_INDEL;
public final static Set<String> PASSES_FILTERS = Collections.unmodifiableSet(new LinkedHashSet<String>());
/** The location of this VariantContext */
protected String contig;
protected long start;
protected long stop;
final protected String contig;
final protected long start;
final protected long stop;
private final String ID;
/** The type (cached for performance reasons) of this context */
protected Type type = null;
@ -199,7 +202,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
private Allele ALT = null;
// were filters applied?
private boolean filtersWereAppliedToContext;
final private boolean filtersWereAppliedToContext;
// ---------------------------------------------------------------------------------------------------------
//
@ -223,10 +226,16 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param attributes attributes
* @param referenceBaseForIndel padded reference base
*/
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, GenotypeCollection genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes, Byte referenceBaseForIndel) {
this(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, referenceBaseForIndel, false, true);
public VariantContext(String source, String ID, String contig, long start, long stop, Collection<Allele> alleles, GenotypeCollection genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes, Byte referenceBaseForIndel) {
this(source, ID, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, referenceBaseForIndel, false, true);
}
@Deprecated
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, GenotypeCollection genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes, Byte referenceBaseForIndel) {
this(source, VCFConstants.EMPTY_ID_FIELD, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, referenceBaseForIndel);
}
/**
* the complete constructor. Makes a complete VariantContext from its arguments
*
@ -240,8 +249,13 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param filters filters: use null for unfiltered and empty set for passes filters
* @param attributes attributes
*/
public VariantContext(String source, String ID, String contig, long start, long stop, Collection<Allele> alleles, GenotypeCollection genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
this(source, ID, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, null, false, true);
}
@Deprecated
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, GenotypeCollection genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
this(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, null, false, true);
this(source, VCFConstants.EMPTY_ID_FIELD, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes);
}
/**
@ -261,8 +275,13 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param attributes attributes
* @param referenceBaseForIndel padded reference base
*/
public VariantContext(String source, String ID, String contig, long start, long stop, Collection<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, Object> attributes, Byte referenceBaseForIndel) {
this(source, ID, contig, start, stop, alleles, NO_GENOTYPES, negLog10PError, filters, attributes, referenceBaseForIndel, true, true);
}
@Deprecated
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, Object> attributes, Byte referenceBaseForIndel) {
this(source, contig, start, stop, alleles, NO_GENOTYPES, negLog10PError, filters, attributes, referenceBaseForIndel, true, true);
this(source, VCFConstants.EMPTY_ID_FIELD, contig, start, stop, alleles, negLog10PError, filters, attributes, referenceBaseForIndel);
}
/**
@ -278,12 +297,19 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param filters filters: use null for unfiltered and empty set for passes filters
* @param attributes attributes
*/
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
this(source, contig, start, stop, alleles,
public VariantContext(String source, String ID, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
this(source, ID, contig, start, stop, alleles,
GenotypeCollection.copy(genotypes),
negLog10PError, filters, attributes, null, false, true);
}
@Deprecated
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
this(source, VCFConstants.EMPTY_ID_FIELD, contig, start, stop, alleles,
GenotypeCollection.copy(genotypes),
negLog10PError, filters, attributes);
}
/**
* Create a new variant context without genotypes and no Perror, no filters, and no attributes
*
@ -293,8 +319,13 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param stop the stop reference base (one based)
* @param alleles alleles
*/
public VariantContext(String source, String ID, String contig, long start, long stop, Collection<Allele> alleles) {
this(source, ID, contig, start, stop, alleles, NO_GENOTYPES, CommonInfo.NO_NEG_LOG_10PERROR, null, null, null, false, true);
}
@Deprecated
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles) {
this(source, contig, start, stop, alleles, NO_GENOTYPES, CommonInfo.NO_NEG_LOG_10PERROR, null, null, null, false, true);
this(source, VCFConstants.EMPTY_ID_FIELD, contig, start, stop, alleles);
}
/**
@ -307,8 +338,13 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param alleles alleles
* @param genotypes genotypes
*/
public VariantContext(String source, String ID, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes) {
this(source, ID, contig, start, stop, alleles, genotypes, CommonInfo.NO_NEG_LOG_10PERROR, null, null);
}
@Deprecated
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes) {
this(source, contig, start, stop, alleles, genotypes, CommonInfo.NO_NEG_LOG_10PERROR, null, null);
this(source, VCFConstants.EMPTY_ID_FIELD, contig, start, stop, alleles, genotypes, CommonInfo.NO_NEG_LOG_10PERROR, null, null);
}
/**
@ -317,7 +353,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param other the VariantContext to copy
*/
public VariantContext(VariantContext other) {
this(other.getSource(), other.getChr(), other.getStart(), other.getEnd() , other.getAlleles(), other.getGenotypes(), other.getNegLog10PError(), other.filtersWereApplied() ? other.getFilters() : null, other.getAttributes(), other.REFERENCE_BASE_FOR_INDEL, false, true);
this(other.getSource(), other.getID(), other.getChr(), other.getStart(), other.getEnd() , other.getAlleles(), other.getGenotypes(), other.getNegLog10PError(), other.filtersWereApplied() ? other.getFilters() : null, other.getAttributes(), other.REFERENCE_BASE_FOR_INDEL, false, true);
}
/**
@ -336,7 +372,8 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param genotypesAreUnparsed true if the genotypes have not yet been parsed
* @param performValidation if true, call validate() as the final step in construction
*/
private VariantContext(String source, String contig, long start, long stop,
private VariantContext(String source, String ID,
String contig, long start, long stop,
Collection<Allele> alleles, GenotypeCollection genotypes,
double negLog10PError, Set<String> filters, Map<String, Object> attributes,
Byte referenceBaseForIndel, boolean genotypesAreUnparsed,
@ -346,6 +383,10 @@ public class VariantContext implements Feature { // to enable tribble intergrati
this.start = start;
this.stop = stop;
// intern for efficiency. equals calls will generate NPE if ID is inappropriately passed in as null
this.ID = ID.equals(VCFConstants.EMPTY_ID_FIELD) ? VCFConstants.EMPTY_ID_FIELD : ID;
if ( this.ID.equals("") ) throw new IllegalArgumentException("ID field cannot be the empty string");
if ( !genotypesAreUnparsed && attributes != null ) {
if ( attributes.containsKey(UNPARSED_GENOTYPE_MAP_KEY) )
attributes.remove(UNPARSED_GENOTYPE_MAP_KEY);
@ -357,13 +398,17 @@ public class VariantContext implements Feature { // to enable tribble intergrati
filtersWereAppliedToContext = filters != null;
REFERENCE_BASE_FOR_INDEL = referenceBaseForIndel;
// todo -- remove me when this check is no longer necessary
if ( this.commonInfo.hasAttribute(ID_KEY) )
throw new IllegalArgumentException("Trying to create a VariantContext with a ID key. Please use provided constructor argument ID");
if ( alleles == null ) { throw new IllegalArgumentException("Alleles cannot be null"); }
// we need to make this a LinkedHashSet in case the user prefers a given ordering of alleles
this.alleles = makeAlleles(alleles);
if ( genotypes == null ) {
genotypes = NO_GENOTYPES;
this.genotypes = NO_GENOTYPES;
} else {
this.genotypes = genotypes.immutable();
}
@ -397,13 +442,13 @@ public class VariantContext implements Feature { // to enable tribble intergrati
// ---------------------------------------------------------------------------------------------------------
public static VariantContext modifyGenotypes(VariantContext vc, GenotypeCollection genotypes) {
VariantContext modifiedVC = new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes(), vc.getReferenceBaseForIndel(), false, false);
VariantContext modifiedVC = new VariantContext(vc.getSource(), vc.getID(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes(), vc.getReferenceBaseForIndel(), false, false);
modifiedVC.validateGenotypes();
return modifiedVC;
}
public static VariantContext modifyLocation(VariantContext vc, String chr, int start, int end) {
VariantContext modifiedVC = new VariantContext(vc.getSource(), chr, start, end, vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes(), vc.getReferenceBaseForIndel(), true, false);
VariantContext modifiedVC = new VariantContext(vc.getSource(), vc.getID(), chr, start, end, vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes(), vc.getReferenceBaseForIndel(), true, false);
// Since start and end have changed, we need to call both validateAlleles() and validateReferencePadding(),
// since those validation routines rely on the values of start and end:
@ -414,31 +459,31 @@ public class VariantContext implements Feature { // to enable tribble intergrati
}
public static VariantContext modifyFilters(VariantContext vc, Set<String> filters) {
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd() , vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), filters, new HashMap<String, Object>(vc.getAttributes()), vc.getReferenceBaseForIndel(), true, false);
return new VariantContext(vc.getSource(), vc.getID(), vc.getChr(), vc.getStart(), vc.getEnd() , vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), filters, new HashMap<String, Object>(vc.getAttributes()), vc.getReferenceBaseForIndel(), true, false);
}
public static VariantContext modifyAttributes(VariantContext vc, Map<String, Object> attributes) {
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, attributes, vc.getReferenceBaseForIndel(), true, false);
return new VariantContext(vc.getSource(), vc.getID(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, attributes, vc.getReferenceBaseForIndel(), true, false);
}
public static VariantContext modifyAttribute(VariantContext vc, final String key, final Object value) {
Map<String, Object> attributes = new HashMap<String, Object>(vc.getAttributes());
attributes.put(key, value);
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, attributes, vc.getReferenceBaseForIndel(), true, false);
return new VariantContext(vc.getSource(), vc.getID(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, attributes, vc.getReferenceBaseForIndel(), true, false);
}
public static VariantContext modifyReferencePadding(VariantContext vc, Byte b) {
VariantContext modifiedVC = new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes(), b, true, false);
VariantContext modifiedVC = new VariantContext(vc.getSource(), vc.getID(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes(), b, true, false);
modifiedVC.validateReferencePadding();
return modifiedVC;
}
public static VariantContext modifyPErrorFiltersAndAttributes(VariantContext vc, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, negLog10PError, filters, attributes, vc.getReferenceBaseForIndel(), true, false);
return new VariantContext(vc.getSource(), vc.getID(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, negLog10PError, filters, attributes, vc.getReferenceBaseForIndel(), true, false);
}
public static VariantContext modifyID(final VariantContext vc, final String id) {
return modifyAttribute(vc, ID_KEY, id);
return new VariantContext(vc.getSource(), id, vc.getChr(), vc.getStart(), vc.getEnd() , vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, new HashMap<String, Object>(vc.getAttributes()), vc.getReferenceBaseForIndel(), true, false);
}
// ---------------------------------------------------------------------------------------------------------
@ -494,7 +539,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
// }
public VariantContext subContextFromSamples(Set<String> sampleNames, Collection<Allele> alleles) {
return new VariantContext(getSource(), contig, start, stop, alleles,
return new VariantContext(getSource(), getID(), contig, start, stop, alleles,
genotypes.subsetToSamples(sampleNames),
getNegLog10PError(),
filtersWereApplied() ? getFilters() : null,
@ -504,7 +549,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
public VariantContext subContextFromSamples(Set<String> sampleNames) {
GenotypeCollection newGenotypes = genotypes.subsetToSamples(sampleNames);
return new VariantContext(getSource(), contig, start, stop, allelesOfGenotypes(newGenotypes),
return new VariantContext(getSource(), getID(), contig, start, stop, allelesOfGenotypes(newGenotypes),
newGenotypes,
getNegLog10PError(),
filtersWereApplied() ? getFilters() : null,
@ -694,11 +739,15 @@ public class VariantContext implements Feature { // to enable tribble intergrati
// ---------------------------------------------------------------------------------------------------------
public boolean hasID() {
return commonInfo.hasAttribute(ID_KEY);
return getID() != VCFConstants.EMPTY_ID_FIELD;
}
public boolean emptyID() {
return ! hasID();
}
public String getID() {
return (String)commonInfo.getAttribute(ID_KEY);
return ID;
}
public boolean hasReferenceBaseForIndel() {
@ -1154,7 +1203,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
}
public void validateRSIDs(Set<String> rsIDs) {
if ( rsIDs != null && hasAttribute(VariantContext.ID_KEY) ) {
if ( rsIDs != null && hasID() ) {
for ( String id : getID().split(VCFConstants.ID_FIELD_SEPARATOR) ) {
if ( id.startsWith("rs") && !rsIDs.contains(id) )
throw new TribbleException.InternalCodecException(String.format("the rsID %s for the record at position %s:%d is not in dbSNP", id, getChr(), getStart()));
@ -1538,7 +1587,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
// Do not change the filter state if filters were not applied to this context
Set<String> inputVCFilters = inputVC.filtersWereAppliedToContext ? inputVC.getFilters() : null;
return new VariantContext(inputVC.getSource(), inputVC.getChr(), inputVC.getStart(), inputVC.getEnd(), alleles, genotypes, inputVC.getNegLog10PError(), inputVCFilters, inputVC.getAttributes(),refByte);
return new VariantContext(inputVC.getSource(), inputVC.getID(), inputVC.getChr(), inputVC.getStart(), inputVC.getEnd(), alleles, genotypes, inputVC.getNegLog10PError(), inputVCFilters, inputVC.getAttributes(),refByte);
}
else
return inputVC;

92
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -57,55 +57,6 @@ public class VariantContextUtils {
engine.setLenient(false);
}
/**
* Create a new VariantContext
*
* @param name name
* @param loc location
* @param alleles alleles
* @param genotypes genotypes set
* @param negLog10PError qual
* @param filters filters: use null for unfiltered and empty set for passes filters
* @param attributes attributes
* @return VariantContext object
*/
public static VariantContext toVC(String name, GenomeLoc loc, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
return new VariantContext(name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, GenotypeCollection.copy(genotypes), negLog10PError, filters, attributes);
}
/**
* Create a new variant context without genotypes and no Perror, no filters, and no attributes
* @param name name
* @param loc location
* @param alleles alleles
* @return VariantContext object
*/
public static VariantContext toVC(String name, GenomeLoc loc, Collection<Allele> alleles) {
return new VariantContext (name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, VariantContext.NO_GENOTYPES, CommonInfo.NO_NEG_LOG_10PERROR, null, null);
}
/**
* Create a new variant context without genotypes and no Perror, no filters, and no attributes
* @param name name
* @param loc location
* @param alleles alleles
* @param genotypes genotypes
* @return VariantContext object
*/
public static VariantContext toVC(String name, GenomeLoc loc, Collection<Allele> alleles, Collection<Genotype> genotypes) {
return new VariantContext(name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, CommonInfo.NO_NEG_LOG_10PERROR, null, null);
}
/**
* Copy constructor
*
* @param other the VariantContext to copy
* @return VariantContext object
*/
public static VariantContext toVC(VariantContext other) {
return new VariantContext(other.getSource(), other.getChr(), other.getStart(), other.getEnd(), other.getAlleles(), other.getGenotypes(), other.getNegLog10PError(), other.getFilters(), other.getAttributes());
}
/**
* Update the attributes of the attributes map given the VariantContext to reflect the proper chromosome-based VCF tags
*
@ -345,19 +296,15 @@ public class VariantContextUtils {
// VC info
final Map<String, Object> attributes = subsetAttributes(vc.commonInfo, keysToPreserve);
// this must be done as the ID is stored in the attributes field
// todo -- remove me when ID becomes a first class field in VC
if ( vc.hasID() ) attributes.put(VariantContext.ID_KEY, vc.getID());
// Genotypes
final GenotypeCollection genotypes = GenotypeCollection.create(vc.getNSamples());
for ( final Genotype g : vc.getGenotypes() ) {
Map<String, Object> genotypeAttributes = subsetAttributes(g.commonInfo, keysToPreserve);
genotypes.add(new Genotype(g.getSampleName(), g.getAlleles(), g.getNegLog10PError(), g.getFilters(),
genotypeAttributes, g.isPhased()));
genotypeAttributes, g.isPhased()));
}
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(),
return new VariantContext(vc.getSource(), vc.getID(), vc.getChr(), vc.getStart(), vc.getEnd(),
vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.getFilters(), attributes);
}
@ -494,7 +441,7 @@ public class VariantContextUtils {
//
if (vc.hasAttribute(VCFConstants.DEPTH_KEY))
depth += vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0);
if ( vc.hasID() && ! vc.getID().equals(VCFConstants.EMPTY_ID_FIELD) ) rsIDs.add(vc.getID());
if ( vc.hasID() ) rsIDs.add(vc.getID());
if (mergeInfoWithMaxAC && vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) {
String rawAlleleCounts = vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY, null);
// lets see if the string contains a , separator
@ -587,11 +534,9 @@ public class VariantContextUtils {
if ( depth > 0 )
attributes.put(VCFConstants.DEPTH_KEY, String.valueOf(depth));
if ( ! rsIDs.isEmpty() ) {
attributes.put(VariantContext.ID_KEY, Utils.join(",", rsIDs));
}
final String ID = rsIDs.isEmpty() ? VCFConstants.EMPTY_ID_FIELD : Utils.join(",", rsIDs);
VariantContext merged = new VariantContext(name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, negLog10PError, filters, (mergeInfoWithMaxAC ? attributesWithMaxAC : attributes) );
VariantContext merged = new VariantContext(name, ID, loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, negLog10PError, filters, (mergeInfoWithMaxAC ? attributesWithMaxAC : attributes) );
// Trim the padded bases of all alleles if necessary
merged = createVariantContextWithTrimmedAlleles(merged);
@ -694,7 +639,7 @@ public class VariantContextUtils {
genotypes.add(Genotype.modifyAlleles(genotype, trimmedAlleles));
}
return new VariantContext(inputVC.getSource(), inputVC.getChr(), inputVC.getStart(), inputVC.getEnd(), alleles, genotypes, inputVC.getNegLog10PError(), inputVC.filtersWereApplied() ? inputVC.getFilters() : null, attributes, new Byte(inputVC.getReference().getBases()[0]));
return new VariantContext(inputVC.getSource(), inputVC.getID(), inputVC.getChr(), inputVC.getStart(), inputVC.getEnd(), alleles, genotypes, inputVC.getNegLog10PError(), inputVC.filtersWereApplied() ? inputVC.getFilters() : null, attributes, new Byte(inputVC.getReference().getBases()[0]));
}
@ -934,7 +879,7 @@ public class VariantContextUtils {
newGenotypes.add(Genotype.modifyAlleles(genotype, newAlleles));
}
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), alleleMap.values(), newGenotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes());
return new VariantContext(vc.getSource(), vc.getID(), vc.getChr(), vc.getStart(), vc.getEnd(), alleleMap.values(), newGenotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes());
}
@ -1058,7 +1003,14 @@ public class VariantContextUtils {
Set<String> mergedFilters = new HashSet<String>(); // Since vc1 and vc2 were unfiltered, the merged record remains unfiltered
Map<String, Object> mergedAttribs = VariantContextUtils.mergeVariantContextAttributes(vc1, vc2);
VariantContext mergedVc = new VariantContext(mergedName, vc1.getChr(), vc1.getStart(), vc2.getEnd(), mergeData.getAllMergedAlleles(), mergedGenotypes, mergedNegLog10PError, mergedFilters, mergedAttribs);
// ids
List<String> mergedIDs = new ArrayList<String>();
if ( vc1.hasID() ) mergedIDs.add(vc1.getID());
if ( vc2.hasID() ) mergedIDs.add(vc2.getID());
String mergedID = Utils.join(VCFConstants.ID_FIELD_SEPARATOR, mergedIDs);
// TODO -- FIX ID
VariantContext mergedVc = new VariantContext(mergedName, mergedID, vc1.getChr(), vc1.getStart(), vc2.getEnd(), mergeData.getAllMergedAlleles(), mergedGenotypes, mergedNegLog10PError, mergedFilters, mergedAttribs);
mergedAttribs = new HashMap<String, Object>(mergedVc.getAttributes());
VariantContextUtils.calculateChromosomeCounts(mergedVc, mergedAttribs, true);
@ -1154,20 +1106,6 @@ public class VariantContextUtils {
mergedAttribs.put(orAttrib, attribVal);
}
// Merge ID fields:
String iDVal = null;
for (VariantContext vc : vcList) {
String val = vc.getAttributeAsString(VariantContext.ID_KEY, null);
if (val != null && !val.equals(VCFConstants.EMPTY_ID_FIELD)) {
if (iDVal == null)
iDVal = val;
else
iDVal += VCFConstants.ID_FIELD_SEPARATOR + val;
}
}
if (iDVal != null)
mergedAttribs.put(VariantContext.ID_KEY, iDVal);
return mergedAttribs;
}

7
public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java
View File

@ -36,6 +36,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@ -65,9 +66,9 @@ public class RefMetaDataTrackerUnitTest {
C = Allele.create("C");
G = Allele.create("G");
T = Allele.create("T");
AC_SNP = new VariantContext("x", "chr1", START_POS, START_POS, Arrays.asList(A, C));
AG_SNP = new VariantContext("x", "chr1", START_POS, START_POS, Arrays.asList(A, G));
AT_SNP = new VariantContext("x", "chr1", START_POS, START_POS, Arrays.asList(A, T));
AC_SNP = new VariantContext("x", VCFConstants.EMPTY_ID_FIELD, "chr1", START_POS, START_POS, Arrays.asList(A, C));
AG_SNP = new VariantContext("x", VCFConstants.EMPTY_ID_FIELD, "chr1", START_POS, START_POS, Arrays.asList(A, G));
AT_SNP = new VariantContext("x", VCFConstants.EMPTY_ID_FIELD, "chr1", START_POS, START_POS, Arrays.asList(A, T));
span10_10 = makeSpan(10, 10);
span1_20 = makeSpan(1, 20);
span10_20 = makeSpan(10, 20);

2
public/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
View File

@ -136,7 +136,7 @@ public class VCFWriterUnitTest extends BaseTest {
genotypes.add(gt);
}
return new VariantContext("RANDOM",loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, 0, filters, attributes, (byte)'A');
return new VariantContext("RANDOM", VCFConstants.EMPTY_ID_FIELD, loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, 0, filters, attributes, (byte)'A');
}

77
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
View File

@ -6,6 +6,7 @@ package org.broadinstitute.sting.utils.variantcontext;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.testng.annotations.BeforeSuite;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
@ -67,68 +68,68 @@ public class VariantContextUnitTest extends BaseTest {
// test REF
List<Allele> alleles = Arrays.asList(Tref);
VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles);
VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles);
Assert.assertEquals(vc.getType(), VariantContext.Type.NO_VARIATION);
// test SNPs
alleles = Arrays.asList(Tref, A);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles);
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles);
Assert.assertEquals(vc.getType(), VariantContext.Type.SNP);
alleles = Arrays.asList(Tref, A, C);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles);
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles);
Assert.assertEquals(vc.getType(), VariantContext.Type.SNP);
// test MNPs
alleles = Arrays.asList(ACref, TA);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles);
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+1, alleles);
Assert.assertEquals(vc.getType(), VariantContext.Type.MNP);
alleles = Arrays.asList(ATCref, CAT, Allele.create("GGG"));
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles);
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+2, alleles);
Assert.assertEquals(vc.getType(), VariantContext.Type.MNP);
// test INDELs
alleles = Arrays.asList(Aref, ATC);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
alleles = Arrays.asList(ATCref, A);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+2, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
alleles = Arrays.asList(Tref, TA, TC);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
alleles = Arrays.asList(ATCref, A, AC);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+2, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
alleles = Arrays.asList(ATCref, A, Allele.create("ATCTC"));
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+2, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
// test MIXED
alleles = Arrays.asList(TAref, T, TC);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+1, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
alleles = Arrays.asList(TAref, T, AC);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+1, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
alleles = Arrays.asList(ACref, ATC, AT);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop+1, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
alleles = Arrays.asList(Aref, T, symbolic);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
// test SYMBOLIC
alleles = Arrays.asList(Tref, symbolic);
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getType(), VariantContext.Type.SYMBOLIC);
}
@ -136,8 +137,8 @@ public class VariantContextUnitTest extends BaseTest {
public void testMultipleSNPAlleleOrdering() {
final List<Allele> allelesNaturalOrder = Arrays.asList(Aref, C, T);
final List<Allele> allelesUnnaturalOrder = Arrays.asList(Aref, T, C);
VariantContext naturalVC = new VariantContext("natural", snpLoc, snpLocStart, snpLocStop, allelesNaturalOrder);
VariantContext unnaturalVC = new VariantContext("unnatural", snpLoc, snpLocStart, snpLocStop, allelesUnnaturalOrder);
VariantContext naturalVC = new VariantContext("natural", VCFConstants.EMPTY_ID_FIELD, snpLoc, snpLocStart, snpLocStop, allelesNaturalOrder);
VariantContext unnaturalVC = new VariantContext("unnatural", VCFConstants.EMPTY_ID_FIELD, snpLoc, snpLocStart, snpLocStop, allelesUnnaturalOrder);
Assert.assertEquals(new ArrayList<Allele>(naturalVC.getAlleles()), allelesNaturalOrder);
Assert.assertEquals(new ArrayList<Allele>(unnaturalVC.getAlleles()), allelesUnnaturalOrder);
}
@ -146,7 +147,7 @@ public class VariantContextUnitTest extends BaseTest {
public void testCreatingSNPVariantContext() {
List<Allele> alleles = Arrays.asList(Aref, T);
VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles);
VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles);
Assert.assertEquals(vc.getChr(), snpLoc);
Assert.assertEquals(vc.getStart(), snpLocStart);
@ -173,7 +174,7 @@ public class VariantContextUnitTest extends BaseTest {
@Test
public void testCreatingRefVariantContext() {
List<Allele> alleles = Arrays.asList(Aref);
VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles);
VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles);
Assert.assertEquals(vc.getChr(), snpLoc);
Assert.assertEquals(vc.getStart(), snpLocStart);
@ -199,7 +200,7 @@ public class VariantContextUnitTest extends BaseTest {
@Test
public void testCreatingDeletionVariantContext() {
List<Allele> alleles = Arrays.asList(ATCref, del);
VariantContext vc = new VariantContext("test", delLoc, delLocStart, delLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, delLoc, delLocStart, delLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getChr(), delLoc);
Assert.assertEquals(vc.getStart(), delLocStart);
@ -226,7 +227,7 @@ public class VariantContextUnitTest extends BaseTest {
@Test
public void testCreatingInsertionVariantContext() {
List<Allele> alleles = Arrays.asList(delRef, ATC);
VariantContext vc = new VariantContext("test", insLoc, insLocStart, insLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, insLoc, insLocStart, insLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getChr(), insLoc);
Assert.assertEquals(vc.getStart(), insLocStart);
@ -253,7 +254,7 @@ public class VariantContextUnitTest extends BaseTest {
public void testCreatingPartiallyCalledGenotype() {
List<Allele> alleles = Arrays.asList(Aref, C);
Genotype g = new Genotype("foo", Arrays.asList(C, Allele.NO_CALL), 10);
VariantContext vc = new VariantContext("test", snpLoc, snpLocStart, snpLocStop, alleles, Arrays.asList(g));
VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc, snpLocStart, snpLocStop, alleles, Arrays.asList(g));
Assert.assertTrue(vc.isSNP());
Assert.assertEquals(vc.getNAlleles(), 2);
@ -274,38 +275,38 @@ public class VariantContextUnitTest extends BaseTest {
@Test (expectedExceptions = IllegalArgumentException.class)
public void testBadConstructorArgs1() {
new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, ATCref));
new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, insLoc, insLocStart, insLocStop, Arrays.asList(delRef, ATCref));
}
@Test (expectedExceptions = IllegalArgumentException.class)
public void testBadConstructorArgs2() {
new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(delRef, del));
new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, insLoc, insLocStart, insLocStop, Arrays.asList(delRef, del));
}
@Test (expectedExceptions = IllegalArgumentException.class)
public void testBadConstructorArgs3() {
new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(del));
new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, insLoc, insLocStart, insLocStop, Arrays.asList(del));
}
@Test (expectedExceptions = IllegalArgumentException.class)
public void testBadConstructorArgs4() {
new VariantContext("test", insLoc, insLocStart, insLocStop, Collections.<Allele>emptyList());
new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, insLoc, insLocStart, insLocStop, Collections.<Allele>emptyList());
}
@Test (expectedExceptions = IllegalArgumentException.class)
public void testBadConstructorArgsDuplicateAlleles1() {
new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(Aref, T, T));
new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, insLoc, insLocStart, insLocStop, Arrays.asList(Aref, T, T));
}
@Test (expectedExceptions = IllegalArgumentException.class)
public void testBadConstructorArgsDuplicateAlleles2() {
new VariantContext("test", insLoc, insLocStart, insLocStop, Arrays.asList(Aref, A));
new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, insLoc, insLocStart, insLocStop, Arrays.asList(Aref, A));
}
@Test (expectedExceptions = IllegalStateException.class)
public void testBadLoc1() {
List<Allele> alleles = Arrays.asList(Aref, T, del);
new VariantContext("test", delLoc, delLocStart, delLocStop, alleles);
new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, delLoc, delLocStart, delLocStop, alleles);
}
@Test
@ -316,7 +317,7 @@ public class VariantContextUnitTest extends BaseTest {
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10);
VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1, g2, g3));
VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1, g2, g3));
Assert.assertTrue(vc.hasGenotypes());
Assert.assertFalse(vc.isMonomorphic());
@ -355,7 +356,7 @@ public class VariantContextUnitTest extends BaseTest {
Genotype g5 = new Genotype("dd", Arrays.asList(del, del), 10);
Genotype g6 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), 10);
VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1, g2, g3, g4, g5, g6));
VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1, g2, g3, g4, g5, g6));
Assert.assertTrue(vc.hasGenotypes());
Assert.assertFalse(vc.isMonomorphic());
@ -380,7 +381,7 @@ public class VariantContextUnitTest extends BaseTest {
Genotype g1 = new Genotype("AA1", Arrays.asList(Aref, Aref), 10);
Genotype g2 = new Genotype("AA2", Arrays.asList(Aref, Aref), 10);
Genotype g3 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), 10);
VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1, g2, g3));
VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1, g2, g3));
Assert.assertTrue(vc.hasGenotypes());
Assert.assertTrue(vc.isMonomorphic());
@ -400,21 +401,21 @@ public class VariantContextUnitTest extends BaseTest {
Genotype g1 = new Genotype("AA", Arrays.asList(Aref, Aref), 10);
Genotype g2 = new Genotype("AT", Arrays.asList(Aref, T), 10);
VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1,g2));
VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1,g2));
Assert.assertTrue(vc.isNotFiltered());
Assert.assertFalse(vc.isFiltered());
Assert.assertEquals(0, vc.getFilters().size());
Set<String> filters = new HashSet<String>(Arrays.asList("BAD_SNP_BAD!"));
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1,g2), VariantContext.NO_NEG_LOG_10PERROR, filters, null);
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1,g2), VariantContext.NO_NEG_LOG_10PERROR, filters, null);
Assert.assertFalse(vc.isNotFiltered());
Assert.assertTrue(vc.isFiltered());
Assert.assertEquals(1, vc.getFilters().size());
filters = new HashSet<String>(Arrays.asList("BAD_SNP_BAD!", "REALLY_BAD_SNP", "CHRIST_THIS_IS_TERRIBLE"));
vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1,g2), VariantContext.NO_NEG_LOG_10PERROR, filters, null);
vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop, alleles, Arrays.asList(g1,g2), VariantContext.NO_NEG_LOG_10PERROR, filters, null);
Assert.assertFalse(vc.isNotFiltered());
Assert.assertTrue(vc.isFiltered());
@ -429,9 +430,9 @@ public class VariantContextUnitTest extends BaseTest {
Genotype g3 = new Genotype("TT", Arrays.asList(T, T), 10);
Genotype g4 = new Genotype("..", Arrays.asList(Allele.NO_CALL, Allele.NO_CALL), 10);
Genotype g5 = new Genotype("--", Arrays.asList(del, del), 10);
VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop , alleles, Arrays.asList(g1,g2,g3,g4,g5));
VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc,snpLocStart, snpLocStop , alleles, Arrays.asList(g1,g2,g3,g4,g5));
VariantContext vc12 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName(),g2.getSampleName())));
VariantContext vc12 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName(), g2.getSampleName())));
VariantContext vc1 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName())));
VariantContext vc23 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g2.getSampleName(), g3.getSampleName())));
VariantContext vc4 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g4.getSampleName())));
@ -514,7 +515,7 @@ public class VariantContextUnitTest extends BaseTest {
@Test(dataProvider = "getAlleles")
public void testMergeAlleles(GetAllelesTest cfg) {
final List<Allele> altAlleles = cfg.alleles.subList(1, cfg.alleles.size());
final VariantContext vc = new VariantContext("test", snpLoc, snpLocStart, snpLocStop, cfg.alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
final VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc, snpLocStart, snpLocStop, cfg.alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A');
Assert.assertEquals(vc.getAlleles(), cfg.alleles, "VC alleles not the same as input alleles");
Assert.assertEquals(vc.getNAlleles(), cfg.alleles.size(), "VC getNAlleles not the same as input alleles size");

3
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
View File

@ -26,6 +26,7 @@ package org.broadinstitute.sting.utils.variantcontext;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.testng.Assert;
@ -98,7 +99,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
private VariantContext makeVC(String source, List<Allele> alleles, Collection<Genotype> genotypes, Set<String> filters) {
int start = 10;
int stop = start; // alleles.contains(ATC) ? start + 3 : start;
return new VariantContext(source, "1", start, stop, alleles,
return new VariantContext(source, VCFConstants.EMPTY_ID_FIELD, "1", start, stop, alleles,
GenotypeCollection.copy(genotypes), 1.0, filters, null, Cref.getBases()[0]);
}

3
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java
View File

@ -24,6 +24,7 @@
package org.broadinstitute.sting.utils.variantcontext;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.GenomeLoc;
@ -143,7 +144,7 @@ public class VariantJEXLContextUnitTest extends BaseTest {
private JEXLMap getVarContext() {
List<Allele> alleles = Arrays.asList(Aref, T);
VariantContext vc = new VariantContext("test", snpLoc.getContig(), snpLoc.getStart(), snpLoc.getStop(), alleles);
VariantContext vc = new VariantContext("test", VCFConstants.EMPTY_ID_FIELD, snpLoc.getContig(), snpLoc.getStart(), snpLoc.getStop(), alleles);
return new JEXLMap(Arrays.asList(exp),vc);
}