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1) When quals/GQs are really integers (x.00), strip off the floating points. 

2) Keep track of whether vcf records are unfiltered vs. pass filters in the variant context so we can regenerate the records on output.
3) No more "ID" hard-coded all over the code to set the VariantContext ID.  Use a static variable instead.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3840 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-20 18:01:45 +00:00
parent 0db7fab1a9
commit c6ad26e04f
26 changed files with 150 additions and 127 deletions
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1
java/src/org/broad/tribble/vcf/VCFConstants.java
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@ -81,4 +81,5 @@ public final class VCFConstants {
public static final double MAX_GENOTYPE_QUAL = 99.0; public static final double MAX_GENOTYPE_QUAL = 99.0;
public static final String DOUBLE_PRECISION_FORMAT_STRING = "%.2f"; public static final String DOUBLE_PRECISION_FORMAT_STRING = "%.2f";
public static final String DOUBLE_PRECISION_INT_SUFFIX = ".00";
} }

4
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/Genotype.java
View File

@ -17,11 +17,14 @@ public class Genotype {
protected InferredGeneticContext commonInfo; protected InferredGeneticContext commonInfo;
public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR; public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR;
protected List<Allele> alleles = null; // new ArrayList<Allele>(); protected List<Allele> alleles = null; // new ArrayList<Allele>();
private boolean genotypesArePhased = false; private boolean genotypesArePhased = false;
private boolean filtersWereAppliedToContext;
public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean genotypesArePhased) { public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, boolean genotypesArePhased) {
this.alleles = Collections.unmodifiableList(alleles); this.alleles = Collections.unmodifiableList(alleles);
commonInfo = new InferredGeneticContext(sampleName, negLog10PError, filters, attributes); commonInfo = new InferredGeneticContext(sampleName, negLog10PError, filters, attributes);
filtersWereAppliedToContext = filters != null;
this.genotypesArePhased = genotypesArePhased; this.genotypesArePhased = genotypesArePhased;
validate(); validate();
} }
@ -191,6 +194,7 @@ public class Genotype {
public Set<String> getFilters() { return commonInfo.getFilters(); } public Set<String> getFilters() { return commonInfo.getFilters(); }
public boolean isFiltered() { return commonInfo.isFiltered(); } public boolean isFiltered() { return commonInfo.isFiltered(); }
public boolean isNotFiltered() { return commonInfo.isNotFiltered(); } public boolean isNotFiltered() { return commonInfo.isNotFiltered(); }
public boolean filtersWereApplied() { return filtersWereAppliedToContext; }
public boolean hasNegLog10PError() { return commonInfo.hasNegLog10PError(); } public boolean hasNegLog10PError() { return commonInfo.hasNegLog10PError(); }
public double getNegLog10PError() { return commonInfo.getNegLog10PError(); } public double getNegLog10PError() { return commonInfo.getNegLog10PError(); }
public double getPhredScaledQual() { return commonInfo.getPhredScaledQual(); } public double getPhredScaledQual() { return commonInfo.getPhredScaledQual(); }

65
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContext.java
View File

@ -164,6 +164,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
protected InferredGeneticContext commonInfo = null; protected InferredGeneticContext commonInfo = null;
public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR; public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR;
public final static String REFERENCE_BASE_FOR_INDEL_KEY = "REFERENCE_BASE_FOR_INDEL"; public final static String REFERENCE_BASE_FOR_INDEL_KEY = "REFERENCE_BASE_FOR_INDEL";
public final static String ID_KEY = "ID";
/** The location of this VariantContext */ /** The location of this VariantContext */
private GenomeLoc loc; private GenomeLoc loc;
@ -188,22 +189,32 @@ public class VariantContext implements Feature { // to enable tribble intergrati
// set to the alt allele when biallelic, otherwise == null // set to the alt allele when biallelic, otherwise == null
private Allele ALT = null; private Allele ALT = null;
// were filters applied?
private boolean filtersWereAppliedToContext;
// --------------------------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------------------------
// //
// constructors // constructors
// //
// --------------------------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------------------------
// todo move all of attribute object attributes into Map<> and make special filter value for printing out values when
// emitting VC -> VCF or whatever
/** /**
* the complete constructor. Makes a complete VariantContext from its arguments * the complete constructor. Makes a complete VariantContext from its arguments
*
* @param name name
* @param loc location
* @param alleles alleles
* @param genotypes genotypes map
* @param negLog10PError qual
* @param filters filters: use null for unfiltered and empty set for passes filters
* @param attributes attributes
*/ */
public VariantContext(String name, GenomeLoc loc, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) { public VariantContext(String name, GenomeLoc loc, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
if ( loc == null ) { throw new StingException("GenomeLoc cannot be null"); } if ( loc == null ) { throw new StingException("GenomeLoc cannot be null"); }
this.loc = loc; this.loc = loc;
this.commonInfo = new InferredGeneticContext(name, negLog10PError, filters, attributes); this.commonInfo = new InferredGeneticContext(name, negLog10PError, filters, attributes);
filtersWereAppliedToContext = filters != null;
if ( alleles == null ) { throw new StingException("Alleles cannot be null"); } if ( alleles == null ) { throw new StingException("Alleles cannot be null"); }
// we need to make this a LinkedHashSet in case the user prefers a given ordering of alleles // we need to make this a LinkedHashSet in case the user prefers a given ordering of alleles
@ -228,13 +239,13 @@ public class VariantContext implements Feature { // to enable tribble intergrati
/** /**
* Create a new VariantContext * Create a new VariantContext
* *
* @param name * @param name name
* @param loc * @param loc location
* @param alleles * @param alleles alleles
* @param genotypes * @param genotypes genotypes set
* @param negLog10PError * @param negLog10PError qual
* @param filters * @param filters filters: use null for unfiltered and empty set for passes filters
* @param attributes * @param attributes attributes
*/ */
public VariantContext(String name, GenomeLoc loc, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) { public VariantContext(String name, GenomeLoc loc, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
this(name, loc, alleles, genotypes != null ? genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes) : null, negLog10PError, filters, attributes); this(name, loc, alleles, genotypes != null ? genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes) : null, negLog10PError, filters, attributes);
@ -242,9 +253,9 @@ public class VariantContext implements Feature { // to enable tribble intergrati
/** /**
* Create a new variant context without genotypes and no Perror, no filters, and no attributes * Create a new variant context without genotypes and no Perror, no filters, and no attributes
* @param name * @param name name
* @param loc * @param loc location
* @param alleles * @param alleles alleles
*/ */
public VariantContext(String name, GenomeLoc loc, Collection<Allele> alleles) { public VariantContext(String name, GenomeLoc loc, Collection<Allele> alleles) {
this(name, loc, alleles, NO_GENOTYPES, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null); this(name, loc, alleles, NO_GENOTYPES, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null);
@ -252,9 +263,10 @@ public class VariantContext implements Feature { // to enable tribble intergrati
/** /**
* Create a new variant context without genotypes and no Perror, no filters, and no attributes * Create a new variant context without genotypes and no Perror, no filters, and no attributes
* @param name * @param name name
* @param loc * @param loc location
* @param alleles * @param alleles alleles
* @param genotypes genotypes
*/ */
public VariantContext(String name, GenomeLoc loc, Collection<Allele> alleles, Collection<Genotype> genotypes) { public VariantContext(String name, GenomeLoc loc, Collection<Allele> alleles, Collection<Genotype> genotypes) {
this(name, loc, alleles, genotypes, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null); this(name, loc, alleles, genotypes, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null);
@ -281,8 +293,8 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* genotype and alleles in genotype. This is the right way to test if a single genotype is actually * genotype and alleles in genotype. This is the right way to test if a single genotype is actually
* variant or not. * variant or not.
* *
* @param genotype * @param genotype genotype
* @return * @return vc subcontext
*/ */
public VariantContext subContextFromGenotypes(Genotype genotype) { public VariantContext subContextFromGenotypes(Genotype genotype) {
return subContextFromGenotypes(Arrays.asList(genotype)); return subContextFromGenotypes(Arrays.asList(genotype));
@ -294,17 +306,17 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* genotypes and alleles in these genotypes. This is the right way to test if a single genotype is actually * genotypes and alleles in these genotypes. This is the right way to test if a single genotype is actually
* variant or not. * variant or not.
* *
* @param genotypes * @param genotypes genotypes
* @return * @return vc subcontext
*/ */
public VariantContext subContextFromGenotypes(Collection<Genotype> genotypes) { public VariantContext subContextFromGenotypes(Collection<Genotype> genotypes) {
return new VariantContext(getName(), getLocation(), allelesOfGenotypes(genotypes), genotypes, getNegLog10PError(), getFilters(), getAttributes()); return new VariantContext(getName(), getLocation(), allelesOfGenotypes(genotypes), genotypes, getNegLog10PError(), getFilters(), getAttributes());
} }
/** /**
* helper routnine for subcontext * helper routine for subcontext
* @param genotypes * @param genotypes genotypes
* @return * @return allele set
*/ */
private Set<Allele> allelesOfGenotypes(Collection<Genotype> genotypes) { private Set<Allele> allelesOfGenotypes(Collection<Genotype> genotypes) {
Set<Allele> alleles = new HashSet<Allele>(); Set<Allele> alleles = new HashSet<Allele>();
@ -478,6 +490,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
public Set<String> getFilters() { return commonInfo.getFilters(); } public Set<String> getFilters() { return commonInfo.getFilters(); }
public boolean isFiltered() { return commonInfo.isFiltered(); } public boolean isFiltered() { return commonInfo.isFiltered(); }
public boolean isNotFiltered() { return commonInfo.isNotFiltered(); } public boolean isNotFiltered() { return commonInfo.isNotFiltered(); }
public boolean filtersWereApplied() { return filtersWereAppliedToContext; }
public boolean hasNegLog10PError() { return commonInfo.hasNegLog10PError(); } public boolean hasNegLog10PError() { return commonInfo.hasNegLog10PError(); }
public double getNegLog10PError() { return commonInfo.getNegLog10PError(); } public double getNegLog10PError() { return commonInfo.getNegLog10PError(); }
public double getPhredScaledQual() { return commonInfo.getPhredScaledQual(); } public double getPhredScaledQual() { return commonInfo.getPhredScaledQual(); }
@ -724,7 +737,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
/** /**
* Returns the number of chromosomes carrying any allele in the genotypes (i.e., excluding NO_CALLS * Returns the number of chromosomes carrying any allele in the genotypes (i.e., excluding NO_CALLS
* *
* @return * @return chromosome count
*/ */
public int getChromosomeCount() { public int getChromosomeCount() {
int n = 0; int n = 0;
@ -739,8 +752,8 @@ public class VariantContext implements Feature { // to enable tribble intergrati
/** /**
* Returns the number of chromosomes carrying allele A in the genotypes * Returns the number of chromosomes carrying allele A in the genotypes
* *
* @param a * @param a allele
* @return * @return chromosome count
*/ */
public int getChromosomeCount(Allele a) { public int getChromosomeCount(Allele a) {
int n = 0; int n = 0;

16
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
View File

@ -242,8 +242,8 @@ public class VariantContextUtils {
filters.addAll(vc.getFilters()); filters.addAll(vc.getFilters());
if ( vc.hasAttribute(VCFConstants.DEPTH_KEY) ) if ( vc.hasAttribute(VCFConstants.DEPTH_KEY) )
depth += Integer.valueOf(vc.getAttributeAsString(VCFConstants.DEPTH_KEY)); depth += Integer.valueOf(vc.getAttributeAsString(VCFConstants.DEPTH_KEY));
if ( rsID == null && vc.hasAttribute("ID") ) if ( rsID == null && vc.hasAttribute(VariantContext.ID_KEY) )
rsID = vc.getAttributeAsString("ID"); rsID = vc.getAttributeAsString(VariantContext.ID_KEY);
for ( Map.Entry<String, Object> p : vc.getAttributes().entrySet() ) { for ( Map.Entry<String, Object> p : vc.getAttributes().entrySet() ) {
if ( ! attributes.containsKey(p.getKey()) || attributes.get(p.getKey()).equals(".") ) { // no value if ( ! attributes.containsKey(p.getKey()) || attributes.get(p.getKey()).equals(".") ) { // no value
@ -277,7 +277,7 @@ public class VariantContextUtils {
if ( depth > 0 ) if ( depth > 0 )
attributes.put(VCFConstants.DEPTH_KEY, String.valueOf(depth)); attributes.put(VCFConstants.DEPTH_KEY, String.valueOf(depth));
if ( rsID != null ) if ( rsID != null )
attributes.put("ID", rsID); attributes.put(VariantContext.ID_KEY, rsID);
VariantContext merged = new VariantContext(name, loc, alleles, genotypes, negLog10PError, filters, attributes); VariantContext merged = new VariantContext(name, loc, alleles, genotypes, negLog10PError, filters, attributes);
if ( printMessages && remapped ) System.out.printf("Remapped => %s%n", merged); if ( printMessages && remapped ) System.out.printf("Remapped => %s%n", merged);
@ -431,11 +431,11 @@ public class VariantContextUtils {
} }
public static VariantContext modifyGenotypes(VariantContext vc, Map<String, Genotype> genotypes) { public static VariantContext modifyGenotypes(VariantContext vc, Map<String, Genotype> genotypes) {
return new VariantContext(vc.getName(), vc.getLocation(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.getFilters(), vc.getAttributes()); return new VariantContext(vc.getName(), vc.getLocation(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes());
} }
public static VariantContext modifyLocation(VariantContext vc, GenomeLoc loc) { public static VariantContext modifyLocation(VariantContext vc, GenomeLoc loc) {
return new VariantContext(vc.getName(), loc, vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.getFilters(), vc.getAttributes()); return new VariantContext(vc.getName(), loc, vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, vc.getAttributes());
} }
public static VariantContext modifyFilters(VariantContext vc, Set<String> filters) { public static VariantContext modifyFilters(VariantContext vc, Set<String> filters) {
@ -443,15 +443,15 @@ public class VariantContextUtils {
} }
public static VariantContext modifyAttributes(VariantContext vc, Map<String, Object> attributes) { public static VariantContext modifyAttributes(VariantContext vc, Map<String, Object> attributes) {
return new VariantContext(vc.getName(), vc.getLocation(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.getFilters(), attributes); return new VariantContext(vc.getName(), vc.getLocation(), vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, attributes);
} }
public static Genotype modifyName(Genotype g, String name) { public static Genotype modifyName(Genotype g, String name) {
return new Genotype(name, g.getAlleles(), g.getNegLog10PError(), g.getFilters(), g.getAttributes(), g.genotypesArePhased()); return new Genotype(name, g.getAlleles(), g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, g.getAttributes(), g.genotypesArePhased());
} }
public static Genotype modifyAttributes(Genotype g, Map<String, Object> attributes) { public static Genotype modifyAttributes(Genotype g, Map<String, Object> attributes) {
return new Genotype(g.getSampleName(), g.getAlleles(), g.getNegLog10PError(), g.getFilters(), attributes, g.genotypesArePhased()); return new Genotype(g.getSampleName(), g.getAlleles(), g.getNegLog10PError(), g.filtersWereApplied() ? g.getFilters() : null, attributes, g.genotypesArePhased());
} }
public static VariantContext purgeUnallowedGenotypeAttributes(VariantContext vc, Set<String> allowedAttributes) { public static VariantContext purgeUnallowedGenotypeAttributes(VariantContext vc, Set<String> allowedAttributes) {

4
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
View File

@ -108,7 +108,7 @@ public class VariantContextAdaptors {
} }
Map<String, String> attributes = new HashMap<String, String>(); Map<String, String> attributes = new HashMap<String, String>();
attributes.put("ID", dbsnp.getRsID()); attributes.put(VariantContext.ID_KEY, dbsnp.getRsID());
Collection<Genotype> genotypes = null; Collection<Genotype> genotypes = null;
VariantContext vc = new VariantContext(name, GenomeLocParser.createGenomeLoc(dbsnp.getChr(),dbsnp.getStart(),dbsnp.getEnd()), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes); VariantContext vc = new VariantContext(name, GenomeLocParser.createGenomeLoc(dbsnp.getChr(),dbsnp.getStart(),dbsnp.getEnd()), alleles, genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attributes);
return vc; return vc;
@ -133,7 +133,7 @@ public class VariantContextAdaptors {
Set<String> filters = vcf.isFiltered() ? new HashSet<String>(Arrays.asList(vcf.getFilteringCodes())) : null; Set<String> filters = vcf.isFiltered() ? new HashSet<String>(Arrays.asList(vcf.getFilteringCodes())) : null;
Map<String, String> attributes = new HashMap<String, String>(vcf.getInfoValues()); Map<String, String> attributes = new HashMap<String, String>(vcf.getInfoValues());
attributes.put("ID", vcf.getID()); attributes.put(VariantContext.ID_KEY, vcf.getID());
// add all of the alt alleles // add all of the alt alleles
List<Allele> alleles = new ArrayList<Allele>(); List<Allele> alleles = new ArrayList<Allele>();

62
java/src/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4Codec.java
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@ -260,7 +260,7 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
// validate the fields // validate the fields
validateFields(attributes.keySet(),new ArrayList(infoFields.keySet())); validateFields(attributes.keySet(),new ArrayList(infoFields.keySet()));
attributes.put("ID", id); attributes.put(VariantContext.ID_KEY, id);
return attributes; return attributes;
} }
@ -285,15 +285,9 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
* @return return a double * @return return a double
*/ */
private Double parseQual(String qualString) { private Double parseQual(String qualString) {
if (qualString.equals(VCFConstants.MISSING_VALUE_v4)) if ( qualString.equals(VCFConstants.MISSING_VALUE_v4) || qualString.equals(VCFConstants.MISSING_QUALITY_v3) )
return VariantContext.NO_NEG_LOG_10PERROR; return VariantContext.NO_NEG_LOG_10PERROR;
else { return Double.valueOf(qualString) / 10;
double q = Double.valueOf(qualString);
if ( q == -1 )
return VariantContext.NO_NEG_LOG_10PERROR;
else
return Double.valueOf(qualString) / 10;
}
} }
/** /**
@ -357,36 +351,36 @@ public class VCF4Codec implements FeatureCodec, NameAwareCodec {
* @return a set of the filters applied * @return a set of the filters applied
*/ */
private Set<String> parseFilters(String filterString) { private Set<String> parseFilters(String filterString) {
Set<String> fFields;
// a PASS is simple (no filters) // null for unfiltered
String passString = VCFConstants.PASSES_FILTERS_v3; if ( filterString.equals(VCFConstants.UNFILTERED) )
if (this.version == VCFHeaderVersion.VCF4_0) return null;
passString = VCFConstants.PASSES_FILTERS_v4;
if ( filterString.equals(passString) ) { // empty set for passes filters
return null; LinkedHashSet<String> fFields = new LinkedHashSet<String>();
}
if ( filterString.equals(VCFConstants.UNFILTERED)) { if ( this.version == VCFHeaderVersion.VCF4_0 ) {
return null; if ( filterString.equals(VCFConstants.PASSES_FILTERS_v4) )
} return fFields;
// else do we have the filter string cached? if ( filterString.equals(VCFConstants.PASSES_FILTERS_v3) )
else if (filterHash.containsKey(filterString)) { throw new StingException(VCFConstants.PASSES_FILTERS_v3 + " is an invalid filter name in vcf4.0");
fFields = filterHash.get(filterString); } else if ( filterString.equals(VCFConstants.PASSES_FILTERS_v3) ) {
return fFields;
} }
// do we have the filter string cached?
if ( filterHash.containsKey(filterString) )
return filterHash.get(filterString);
// otherwise we have to parse and cache the value // otherwise we have to parse and cache the value
else { if ( filterString.indexOf(";") == -1 )
LinkedHashSet<String> s = new LinkedHashSet<String>(1); fFields.add(filterString);
if ( filterString.indexOf(";") == -1 ) { else
s.add(filterString); fFields.addAll(Utils.split(filterString, ";"));
} else {
s.addAll(Utils.split(filterString, ";"));
}
filterHash.put(filterString,s);
fFields = s;
}
validateFields(fFields,filterFields); filterHash.put(filterString, fFields);
validateFields(fFields, filterFields);
return fFields; return fFields;
} }

2
java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java
View File

@ -72,7 +72,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
for ( VariantContext vc : contexts ) { for ( VariantContext vc : contexts ) {
Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes()); Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
if ( dbsnp != null ) if ( dbsnp != null )
attrs.put("ID", dbsnp.getRsID()); attrs.put(VariantContext.ID_KEY, dbsnp.getRsID());
vc = VariantContextUtils.modifyAttributes(vc, attrs); vc = VariantContextUtils.modifyAttributes(vc, attrs);
// set the appropriate sample name if necessary // set the appropriate sample name if necessary

6
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
View File

@ -191,8 +191,8 @@ public class VariantAnnotatorEngine {
DbSNPFeature dbsnp = DbSNPHelper.getFirstRealSNP(tracker.getReferenceMetaData(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME)); DbSNPFeature dbsnp = DbSNPHelper.getFirstRealSNP(tracker.getReferenceMetaData(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME));
infoAnnotations.put(VCFConstants.DBSNP_KEY, dbsnp == null ? false : true); infoAnnotations.put(VCFConstants.DBSNP_KEY, dbsnp == null ? false : true);
// annotate dbsnp id if available and not already there // annotate dbsnp id if available and not already there
if ( dbsnp != null && (!vc.hasAttribute("ID") || vc.getAttribute("ID").equals(VCFConstants.EMPTY_ID_FIELD)) ) if ( dbsnp != null && (!vc.hasAttribute(VariantContext.ID_KEY) || vc.getAttribute(VariantContext.ID_KEY).equals(VCFConstants.EMPTY_ID_FIELD)) )
infoAnnotations.put("ID", dbsnp.getRsID()); infoAnnotations.put(VariantContext.ID_KEY, dbsnp.getRsID());
} else { } else {
List<Object> dbRod = tracker.getReferenceMetaData(dbSet.getKey()); List<Object> dbRod = tracker.getReferenceMetaData(dbSet.getKey());
infoAnnotations.put(dbSet.getValue(), dbRod.size() == 0 ? false : true); infoAnnotations.put(dbSet.getValue(), dbRod.size() == 0 ? false : true);
@ -252,7 +252,7 @@ public class VariantAnnotatorEngine {
//Create a separate VariantContext (aka. output line) for each element in infoAnnotationOutputsList //Create a separate VariantContext (aka. output line) for each element in infoAnnotationOutputsList
Collection<VariantContext> returnValue = new LinkedList<VariantContext>(); Collection<VariantContext> returnValue = new LinkedList<VariantContext>();
for(Map<String, Object> infoAnnotationOutput : infoAnnotationOutputsList) { for(Map<String, Object> infoAnnotationOutput : infoAnnotationOutputsList) {
returnValue.add( new VariantContext(vc.getName(), vc.getLocation(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.getFilters(), infoAnnotationOutput) ); returnValue.add( new VariantContext(vc.getName(), vc.getLocation(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, infoAnnotationOutput) );
} }
return returnValue; return returnValue;

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
View File

@ -372,7 +372,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
DbSNPFeature dbsnp = getDbSNP(tracker); DbSNPFeature dbsnp = getDbSNP(tracker);
if ( dbsnp != null ) if ( dbsnp != null )
attributes.put("ID", dbsnp.getRsID()); attributes.put(VariantContext.ID_KEY, dbsnp.getRsID());
if ( !UAC.NO_SLOD ) { if ( !UAC.NO_SLOD ) {
// the overall lod // the overall lod

11
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
View File

@ -321,9 +321,14 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
readsToClean.clear(); readsToClean.clear();
readsNotToClean.clear(); readsNotToClean.clear();
do { try {
currentInterval = intervals.hasNext() ? intervals.next() : null; do {
} while ( currentInterval != null && (readLoc == null || currentInterval.isBefore(readLoc)) ); currentInterval = intervals.hasNext() ? intervals.next() : null;
} while ( currentInterval != null && (readLoc == null || currentInterval.isBefore(readLoc)) );
} catch (StingException e) {
throw new StingException(e.getMessage() + " *** Are you sure that your interval file is sorted? If not, you must use the --targetIntervalsAreNotSorted argument. ***");
}
// call back into map now that the state has been updated // call back into map now that the state has been updated
map(ref, read, metaDataTracker); map(ref, read, metaDataTracker);

2
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverter.java
View File

@ -209,7 +209,7 @@ public class SequenomValidationConverter extends RodWalker<Pair<VariantContext,
// set the id if it's a plink rod // set the id if it's a plink rod
if ( rod instanceof PlinkRod ) if ( rod instanceof PlinkRod )
infoMap.put("ID", ((PlinkRod)rod).getVariantName()); infoMap.put(VariantContext.ID_KEY, ((PlinkRod)rod).getVariantName());
vContext = VariantContextUtils.modifyAttributes(vContext, infoMap); vContext = VariantContextUtils.modifyAttributes(vContext, infoMap);

3
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -353,9 +353,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
return new HashSet<String>(toExclude); return new HashSet<String>(toExclude);
} }
private final static String ID = "ID";
private boolean excludeComp(VariantContext vc) { private boolean excludeComp(VariantContext vc) {
String id = vc != null && vc.hasAttribute(ID) ? vc.getAttributeAsString(ID) : null; String id = vc != null && vc.hasAttribute(VariantContext.ID_KEY) ? vc.getAttributeAsString(VariantContext.ID_KEY) : null;
boolean ex = rsIDsToExclude != null && id != null && rsIDsToExclude.contains(id); boolean ex = rsIDsToExclude != null && id != null && rsIDsToExclude.contains(id);
//System.out.printf("Testing id %s ex=%b against %s%n", id, ex, vc); //System.out.printf("Testing id %s ex=%b against %s%n", id, ex, vc);
return ex; return ex;

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
View File

@ -202,7 +202,7 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
public VariantContext toVariantContext() { public VariantContext toVariantContext() {
newAttributes.putAll(trio.getAttributes()); newAttributes.putAll(trio.getAttributes());
return new VariantContext(trio.getName(),trio.getLocation(),trio.getAlleles(),trio.getGenotypes(),trio.getNegLog10PError(),trio.getFilters(),newAttributes); return new VariantContext(trio.getName(),trio.getLocation(),trio.getAlleles(),trio.getGenotypes(),trio.getNegLog10PError(),trio.filtersWereApplied()?trio.getFilters():null,newAttributes);
} }
public boolean siteIsFiltered() { public boolean siteIsFiltered() {

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/BeagleOutputToVCFWalker.java
View File

@ -284,7 +284,7 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
} }
VariantContext filteredVC = new VariantContext("outputvcf", vc_input.getLocation(), vc_input.getAlleles(), genotypes, vc_input.getNegLog10PError(), vc_input.getFilters(), vc_input.getAttributes()); VariantContext filteredVC = new VariantContext("outputvcf", vc_input.getLocation(), vc_input.getAlleles(), genotypes, vc_input.getNegLog10PError(), vc_input.filtersWereApplied() ? vc_input.getFilters() : null, vc_input.getAttributes());
Set<Allele> altAlleles = filteredVC.getAlternateAlleles(); Set<Allele> altAlleles = filteredVC.getAlternateAlleles();
StringBuffer altAlleleCountString = new StringBuffer(); StringBuffer altAlleleCountString = new StringBuffer();

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java
View File

@ -127,7 +127,7 @@ public class SnpCallRateByCoverageWalker extends LocusWalker<List<String>, Strin
out.printf("%s\t%s\t\t%d\t%f\t%d\t%c\t%s\t%s\t%d\t%d%n", out.printf("%s\t%s\t\t%d\t%f\t%d\t%c\t%s\t%s\t%d\t%d%n",
context.getLocation(), context.getLocation(),
vc.hasAttribute("ID") ? vc.getAttribute("ID") : "?", vc.hasAttribute(VariantContext.ID_KEY) ? vc.getAttribute(VariantContext.ID_KEY) : "?",
coverage, coverage,
((float) coverage)/((float) reads.size()), ((float) coverage)/((float) reads.size()),
goodIterations, goodIterations,

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantoptimizer/AnnotationDataManager.java
View File

@ -84,7 +84,7 @@ public class AnnotationDataManager {
treeSet.add(datum); treeSet.add(datum);
} }
final boolean isNovelVariant = infoField.containsKey("ID"); final boolean isNovelVariant = infoField.containsKey(VariantContext.ID_KEY);
// Decide if the variant is a transition or transversion // Decide if the variant is a transition or transversion
if ( vc.isSNP() ) { if ( vc.isSNP() ) {

19
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFWriter.java
View File

@ -153,7 +153,7 @@ public class VCFWriter {
mWriter.write(VCFConstants.FIELD_SEPARATOR); mWriter.write(VCFConstants.FIELD_SEPARATOR);
// ID // ID
String ID = vc.hasAttribute("ID") ? vc.getAttributeAsString("ID") : VCFConstants.EMPTY_ID_FIELD; String ID = vc.hasAttribute(VariantContext.ID_KEY) ? vc.getAttributeAsString(VariantContext.ID_KEY) : VCFConstants.EMPTY_ID_FIELD;
mWriter.write(ID); mWriter.write(ID);
mWriter.write(VCFConstants.FIELD_SEPARATOR); mWriter.write(VCFConstants.FIELD_SEPARATOR);
@ -186,11 +186,11 @@ public class VCFWriter {
if ( !vc.hasNegLog10PError() ) if ( !vc.hasNegLog10PError() )
mWriter.write(VCFConstants.MISSING_VALUE_v4); mWriter.write(VCFConstants.MISSING_VALUE_v4);
else else
mWriter.write(String.format(VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, vc.getPhredScaledQual())); mWriter.write(getQualValue(vc.getPhredScaledQual()));
mWriter.write(VCFConstants.FIELD_SEPARATOR); mWriter.write(VCFConstants.FIELD_SEPARATOR);
// FILTER // FILTER
String filters = vc.isFiltered() ? Utils.join(";", Utils.sorted(vc.getFilters())) : (filtersWereAppliedToContext ? VCFConstants.PASSES_FILTERS_v4 : VCFConstants.UNFILTERED); String filters = vc.isFiltered() ? Utils.join(";", Utils.sorted(vc.getFilters())) : (filtersWereAppliedToContext || vc.filtersWereApplied() ? VCFConstants.PASSES_FILTERS_v4 : VCFConstants.UNFILTERED);
mWriter.write(filters); mWriter.write(filters);
mWriter.write(VCFConstants.FIELD_SEPARATOR); mWriter.write(VCFConstants.FIELD_SEPARATOR);
@ -198,7 +198,7 @@ public class VCFWriter {
Map<String, String> infoFields = new TreeMap<String, String>(); Map<String, String> infoFields = new TreeMap<String, String>();
for ( Map.Entry<String, Object> field : vc.getAttributes().entrySet() ) { for ( Map.Entry<String, Object> field : vc.getAttributes().entrySet() ) {
String key = field.getKey(); String key = field.getKey();
if ( key.equals("ID") || key.equals(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY) ) if ( key.equals(VariantContext.ID_KEY) || key.equals(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY) )
continue; continue;
String outputValue = formatVCFField(field.getValue()); String outputValue = formatVCFField(field.getValue());
@ -235,6 +235,13 @@ public class VCFWriter {
} }
private String getQualValue(double qual) {
String s = String.format(VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, qual);
if ( s.endsWith(VCFConstants.DOUBLE_PRECISION_INT_SUFFIX) )
s = s.substring(0, s.length() - VCFConstants.DOUBLE_PRECISION_INT_SUFFIX.length());
return s;
}
private String makeAlleleString(Allele allele, boolean isIndel, byte ref) { private String makeAlleleString(Allele allele, boolean isIndel, byte ref) {
String s = new String(allele.getBases()); String s = new String(allele.getBases());
if ( isIndel || s.length() == 0 ) // in case the context is monomorphic at an indel site if ( isIndel || s.length() == 0 ) // in case the context is monomorphic at an indel site
@ -322,14 +329,14 @@ public class VCFWriter {
if ( MathUtils.compareDoubles(g.getNegLog10PError(), Genotype.NO_NEG_LOG_10PERROR) == 0 ) if ( MathUtils.compareDoubles(g.getNegLog10PError(), Genotype.NO_NEG_LOG_10PERROR) == 0 )
val = VCFConstants.MISSING_VALUE_v4; val = VCFConstants.MISSING_VALUE_v4;
else { else {
val = String.format(VCFConstants.DOUBLE_PRECISION_FORMAT_STRING, Math.min(g.getPhredScaledQual(), VCFConstants.MAX_GENOTYPE_QUAL)); val = getQualValue(Math.min(g.getPhredScaledQual(), VCFConstants.MAX_GENOTYPE_QUAL));
} }
} else if ( key.equals(VCFConstants.DEPTH_KEY) && val == null ) { } else if ( key.equals(VCFConstants.DEPTH_KEY) && val == null ) {
ReadBackedPileup pileup = (ReadBackedPileup)g.getAttribute(CalledGenotype.READBACKEDPILEUP_ATTRIBUTE_KEY); ReadBackedPileup pileup = (ReadBackedPileup)g.getAttribute(CalledGenotype.READBACKEDPILEUP_ATTRIBUTE_KEY);
if ( pileup != null ) if ( pileup != null )
val = pileup.size(); val = pileup.size();
} else if ( key.equals(VCFConstants.GENOTYPE_FILTER_KEY) ) { } else if ( key.equals(VCFConstants.GENOTYPE_FILTER_KEY) ) {
val = g.isFiltered() ? Utils.join(";", Utils.sorted(g.getFilters())) : VCFConstants.PASSES_FILTERS_v4; val = g.isFiltered() ? Utils.join(";", Utils.sorted(g.getFilters())) : (g.filtersWereApplied() ? VCFConstants.PASSES_FILTERS_v4 : VCFConstants.UNFILTERED);
} }
VCFFormatHeaderLine metaData = mHeader.getFormatHeaderLine(key); VCFFormatHeaderLine metaData = mHeader.getFormatHeaderLine(key);

2
java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java
View File

@ -48,7 +48,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -B vcf,VCF," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s", WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -B vcf,VCF," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s",
2, // just one output file 2, // just one output file
Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "127941314940d82da4d6f2eb8df43a92")); Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "f4db5f7346792b1155693722bc190f63"));
executeTest("testToVCF", spec); executeTest("testToVCF", spec);
} }

6
java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java
View File

@ -20,7 +20,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test @Test
public void testVariantsToVCFUsingGeliInput() { public void testVariantsToVCFUsingGeliInput() {
List<String> md5 = new ArrayList<String>(); List<String> md5 = new ArrayList<String>();
md5.add("519593d09da03e6503a863dce439151b"); md5.add("b4f98bee580508637c88c421064936fc");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + oneKGLocation + "reference/human_b36_both.fasta" + "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
@ -37,7 +37,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test @Test
public void testGenotypesToVCFUsingGeliInput() { public void testGenotypesToVCFUsingGeliInput() {
List<String> md5 = new ArrayList<String>(); List<String> md5 = new ArrayList<String>();
md5.add("4541686d38eced70b8fb6647551d2329"); md5.add("0f310612c8609cba3dcf9cc97b2c1195");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + oneKGLocation + "reference/human_b36_both.fasta" + "-R " + oneKGLocation + "reference/human_b36_both.fasta" +
@ -70,7 +70,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
@Test @Test
public void testGenotypesToVCFUsingVCFInput() { public void testGenotypesToVCFUsingVCFInput() {
List<String> md5 = new ArrayList<String>(); List<String> md5 = new ArrayList<String>();
md5.add("919eb499bfcc980a14825a0265e575e3"); md5.add("19371e6cfea5f29fb75d5a2be7fccd34");
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + oneKGLocation + "reference/human_b36_both.fasta" + "-R " + oneKGLocation + "reference/human_b36_both.fasta" +

20
java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -15,7 +15,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsNotAsking1() { public void testHasAnnotsNotAsking1() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("8c3db7d5ea580242dda3e9ab1054c150")); Arrays.asList("989ff3afb1384b3c6c8a284b11ebb228"));
executeTest("test file has annotations, not asking for annotations, #1", spec); executeTest("test file has annotations, not asking for annotations, #1", spec);
} }
@ -23,7 +23,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsNotAsking2() { public void testHasAnnotsNotAsking2() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("a7a342c880c81c289d903728080e3e01")); Arrays.asList("5c58506847ddf85bfe75c3cf3babb669"));
executeTest("test file has annotations, not asking for annotations, #2", spec); executeTest("test file has annotations, not asking for annotations, #2", spec);
} }
@ -31,7 +31,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking1() { public void testHasAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("da9fa5c1b2a141286890d5364d87cd4b")); Arrays.asList("184fc1f99dfba3e2519d16458d728fcc"));
executeTest("test file has annotations, asking for annotations, #1", spec); executeTest("test file has annotations, asking for annotations, #1", spec);
} }
@ -39,7 +39,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testHasAnnotsAsking2() { public void testHasAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("513984b5528fde2a835883a6e3d6d2db")); Arrays.asList("12a069d5f1c9cd3970ea6301397219aa"));
executeTest("test file has annotations, asking for annotations, #2", spec); executeTest("test file has annotations, asking for annotations, #2", spec);
} }
@ -47,7 +47,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsNotAsking1() { public void testNoAnnotsNotAsking1() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("2cedac7d2804621107e80a74ac9d01b0")); Arrays.asList("3712b2901bece15094c1eb468dfdc5a8"));
executeTest("test file doesn't have annotations, not asking for annotations, #1", spec); executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
} }
@ -55,7 +55,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsNotAsking2() { public void testNoAnnotsNotAsking2() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("08138975e9c32463e358b86888a84c5e")); Arrays.asList("b7b0e9f3f4f25fd41f388a736dd7b3b8"));
executeTest("test file doesn't have annotations, not asking for annotations, #2", spec); executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
} }
@ -63,7 +63,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking1() { public void testNoAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
Arrays.asList("e2f4031fc005d96af59963bc9833ff76")); Arrays.asList("8f42df642b329ff19bc2c39470117280"));
executeTest("test file doesn't have annotations, asking for annotations, #1", spec); executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
} }
@ -71,7 +71,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoAnnotsAsking2() { public void testNoAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
Arrays.asList("63c99a5e99974793850de225e3410ea6")); Arrays.asList("908aa4b6ac65bee57f91bc6fed4d46ad"));
executeTest("test file doesn't have annotations, asking for annotations, #2", spec); executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
} }
@ -79,7 +79,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testNoReads() { public void testNoReads() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1, baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
Arrays.asList("461e2273b26c9e9c675d1fb8a24df121")); Arrays.asList("24234da54855c892625008fb134e3a88"));
executeTest("not passing it any reads", spec); executeTest("not passing it any reads", spec);
} }
@ -87,7 +87,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
public void testDBTag() { public void testDBTag() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1, baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
Arrays.asList("caa2b55ca2f256dce4b76bad41c29ec5")); Arrays.asList("24d9649943be876e78f76bbf9ff5b501"));
executeTest("getting DB tag", spec); executeTest("getting DB tag", spec);
} }
} }

16
java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
View File

@ -16,7 +16,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testNoAction() { public void testNoAction() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("e0543c72ed36f4c0c43d791ad44aa96a")); Arrays.asList("2cac82e304185cfceea5816f89f64773"));
executeTest("test no action", spec); executeTest("test no action", spec);
} }
@ -24,7 +24,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testClusteredSnps() { public void testClusteredSnps() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -window 10 -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, baseTestString() + " -window 10 -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("2385975931cd06fca452655bebf5c379")); Arrays.asList("5ae28a70de7a778c50749a60b69724ee"));
executeTest("test clustered SNPs", spec); executeTest("test clustered SNPs", spec);
} }
@ -32,7 +32,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testMask() { public void testMask() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -mask foo -B mask,VCF," + validationDataLocation + "vcfexample2.vcf -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, baseTestString() + " -mask foo -B mask,VCF," + validationDataLocation + "vcfexample2.vcf -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("6743efa09985206819adcf8eaf5ff936")); Arrays.asList("0404f10b3c928ee1ea240ccea6ee3cd1"));
executeTest("test mask", spec); executeTest("test mask", spec);
} }
@ -40,7 +40,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testFilter1() { public void testFilter1() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("e054f57d3794ce8a57cae92f16886cf0")); Arrays.asList("fa110840f477b238c0b30ed4fae5ab72"));
executeTest("test filter #1", spec); executeTest("test filter #1", spec);
} }
@ -48,7 +48,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testFilter2() { public void testFilter2() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("db09a1f7ff523087ea0f6a56f3febfe7")); Arrays.asList("9a30dd4c67ddbfadc9e153e0345b46d4"));
executeTest("test filter #2", spec); executeTest("test filter #2", spec);
} }
@ -56,7 +56,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testFilterWithSeparateNames() { public void testFilterWithSeparateNames() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --filterName ABF -filter 'AlleleBalance < 70.0' --filterName FSF -filter 'FisherStrand == 1.4' -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, baseTestString() + " --filterName ABF -filter 'AlleleBalance < 70.0' --filterName FSF -filter 'FisherStrand == 1.4' -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("edbd505d8d55b4ba71f99d7006871db0")); Arrays.asList("7052fca252754e7a92ddb1f27123c7c8"));
executeTest("test filter with separate names #2", spec); executeTest("test filter with separate names #2", spec);
} }
@ -64,7 +64,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testGenotypeFilter1() { public void testGenotypeFilter1() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("391cd1c96546d1760265f7924428af8f")); Arrays.asList("e22ecae2f992fb9d5a91c286f9ac3e40"));
executeTest("test genotype filter #1", spec); executeTest("test genotype filter #1", spec);
} }
@ -72,7 +72,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
public void testGenotypeFilter2() { public void testGenotypeFilter2() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("0eb48f8cb2ad6a0e46c88a5116be2b04")); Arrays.asList("b7e7e7abbf5b03d773f82cced33497a4"));
executeTest("test genotype filter #2", spec); executeTest("test genotype filter #2", spec);
} }
} }

20
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -35,7 +35,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1Joint() { public void testMultiSamplePilot1Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000", 1, "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000", 1,
Arrays.asList("2078bb6eac35f50c346faa0b9c531539")); Arrays.asList("3a402233264e21a84d421e3a4ea64768"));
executeTest("testMultiSamplePilot1 - Joint Estimate", spec); executeTest("testMultiSamplePilot1 - Joint Estimate", spec);
} }
@ -43,7 +43,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot2Joint() { public void testMultiSamplePilot2Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000", 1, "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000", 1,
Arrays.asList("b72f222af1bb7212645822d196ebfc70")); Arrays.asList("79736b3e955a16b30f827b2786fc08b1"));
executeTest("testMultiSamplePilot2 - Joint Estimate", spec); executeTest("testMultiSamplePilot2 - Joint Estimate", spec);
} }
@ -51,7 +51,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testSingleSamplePilot2Joint() { public void testSingleSamplePilot2Joint() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000", 1, "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000", 1,
Arrays.asList("419751fd5f2797db30d8b4442a72613d")); Arrays.asList("b8d93c6fcb4b17d454cdcbfc4b43f076"));
executeTest("testSingleSamplePilot2 - Joint Estimate", spec); executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
} }
@ -63,7 +63,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test @Test
public void testParallelization() { public void testParallelization() {
String md5 = "fc5798b2ef700e60fa032951bab9607d"; String md5 = "098802639cfab1b777c96d38376f118a";
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000", 1, "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000", 1,
@ -90,11 +90,11 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test @Test
public void testParameter() { public void testParameter() {
HashMap<String, String> e = new HashMap<String, String>(); HashMap<String, String> e = new HashMap<String, String>();
e.put( "-genotype", "acae0a31c1f6688bad2fc7f12d66cbc7" ); e.put( "-genotype", "b87f28a772eb75c8dad9062c6d039da5" );
e.put( "-all_bases", "45b50b072385dcbf49bb01299f208d38" ); e.put( "-all_bases", "ec9de2044cd5f5901d6879b56f12993a" );
e.put( "--min_base_quality_score 26", "875c64a64fd402626e04c9540388c483" ); e.put( "--min_base_quality_score 26", "875c64a64fd402626e04c9540388c483" );
e.put( "--min_mapping_quality_score 26", "e1eff3777c392421eea8818c96032206" ); e.put( "--min_mapping_quality_score 26", "de7d90e425f8f08f219dc91a25d60c68" );
e.put( "--max_mismatches_in_40bp_window 5", "8b4239123bd86ccff388472e7909e186" ); e.put( "--max_mismatches_in_40bp_window 5", "758e312b2a2e7c4d83f60174d43fac8a" );
for ( Map.Entry<String, String> entry : e.entrySet() ) { for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -108,12 +108,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testConfidence() { public void testConfidence() {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1, "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
Arrays.asList("6388be650932750426b84c973a3fc04d")); Arrays.asList("4937bab94b0bae1aa61cdf3a06cb49e8"));
executeTest("testConfidence1", spec1); executeTest("testConfidence1", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
"-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1, "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
Arrays.asList("e3f402fbbb6bbb4f60b1aa0549989d85")); Arrays.asList("f8b722dad5c4868a4bba246eef83f96d"));
executeTest("testConfidence2", spec2); executeTest("testConfidence2", spec2);
} }

2
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -118,7 +118,7 @@ public class
for (String tests : testsEnumerations) { for (String tests : testsEnumerations) {
WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s", WalkerTestSpec spec = new WalkerTestSpec(tests + " " + extraArgs + " -o %s -outputVCF %s",
2, 2,
Arrays.asList("483f821ce96f4cf571e9bba356c9f325", "d94328f4a5f7c40e95edf2ef13f38ae0")); Arrays.asList("483f821ce96f4cf571e9bba356c9f325", "989bc30dea6c8a4cf771cd1b9fdab488"));
executeTest("testVEWriteVCF", spec); executeTest("testVEWriteVCF", spec);
} }
} }

2
java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -37,7 +37,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
@Test @Test
public void testVariantRecalibrator() { public void testVariantRecalibrator() {
HashMap<String, String> e = new HashMap<String, String>(); HashMap<String, String> e = new HashMap<String, String>();
e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "a1acb90f0695cbe33c290403113ac3e1" ); e.put( validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "0cb94385ced8a7a537d7bc79f82c01d3" );
for ( Map.Entry<String, String> entry : e.entrySet() ) { for ( Map.Entry<String, String> entry : e.entrySet() ) {
String vcf = entry.getKey(); String vcf = entry.getKey();

2
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -62,7 +62,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
@Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", ""); } @Test public void test1Indel1() { test1InOut("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", ""); }
@Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", ""); } @Test public void test1Indel2() { test1InOut("CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", ""); }
@Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "2ec9e7acff0c36c2b51b2b720944bcde"); } // official project VCF files in tabix format @Test public void combineTrioCalls() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "YRI.trio.2010_03.genotypes.vcf.gz", "02f292cde282ab8b0c69459335abb74f"); } // official project VCF files in tabix format
@Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", ""); } @Test public void combineSNPsAndIndels() { combine2("CEU.trio.2010_03.genotypes.vcf.gz", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", ""); }
@Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", ""); } @Test public void combine2Indels() { combine2("CEU.dindel.vcf4.trio.2010_06.indel.genotypes.vcf", "CEU.dindel.vcf4.low_coverage.2010_06.indel.genotypes.vcf", ""); }

2
java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java
View File

@ -26,7 +26,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
*/ */
String[] md5WithDashSArg = {"454609ac18f149b0175ad99b0ea2d09e"}; String[] md5WithDashSArg = {"94edacdaee0dd58508d35d4d6040e31b"};
WalkerTestSpec specWithSArg = new WalkerTestSpec( WalkerTestSpec specWithSArg = new WalkerTestSpec(
"-T GenomicAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta " + "-T GenomicAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta " +
"-B variant,vcf,/humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf " + "-B variant,vcf,/humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf " +