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Perform only necessary validation in VariantContext modify methods

This commit is contained in:
David Roazen 2011-11-14 15:10:50 -05:00
parent 5c38a9cfd6
commit ab0ee9b847
1 changed files with 34 additions and 14 deletions
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46
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
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@ -223,7 +223,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param referenceBaseForIndel padded reference base * @param referenceBaseForIndel padded reference base
*/ */
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes, Byte referenceBaseForIndel) { public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes, Byte referenceBaseForIndel) {
this(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, referenceBaseForIndel, false); this(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, referenceBaseForIndel, false, true);
} }
/** /**
@ -240,7 +240,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param attributes attributes * @param attributes attributes
*/ */
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) { public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Map<String, Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
this(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, null, false); this(source, contig, start, stop, alleles, genotypes, negLog10PError, filters, attributes, null, false, true);
} }
/** /**
@ -261,7 +261,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param referenceBaseForIndel padded reference base * @param referenceBaseForIndel padded reference base
*/ */
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, Byte referenceBaseForIndel) { public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes, Byte referenceBaseForIndel) {
this(source, contig, start, stop, alleles, NO_GENOTYPES, negLog10PError, filters, attributes, referenceBaseForIndel, true); this(source, contig, start, stop, alleles, NO_GENOTYPES, negLog10PError, filters, attributes, referenceBaseForIndel, true, true);
} }
/** /**
@ -278,7 +278,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param attributes attributes * @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, ?> attributes) { public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
this(source, contig, start, stop, alleles, genotypes != null ? genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes) : null, negLog10PError, filters, attributes, null, false); this(source, contig, start, stop, alleles, genotypes != null ? genotypeCollectionToMap(new TreeMap<String, Genotype>(), genotypes) : null, negLog10PError, filters, attributes, null, false, true);
} }
/** /**
@ -291,7 +291,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param alleles alleles * @param alleles alleles
*/ */
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles) { public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles) {
this(source, contig, start, stop, alleles, NO_GENOTYPES, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, null, false); this(source, contig, start, stop, alleles, NO_GENOTYPES, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, null, false, true);
} }
/** /**
@ -314,7 +314,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param other the VariantContext to copy * @param other the VariantContext to copy
*/ */
public VariantContext(VariantContext other) { 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); 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);
} }
/** /**
@ -331,11 +331,13 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param attributes attributes * @param attributes attributes
* @param referenceBaseForIndel padded reference base * @param referenceBaseForIndel padded reference base
* @param genotypesAreUnparsed true if the genotypes have not yet been parsed * @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 contig, long start, long stop,
Collection<Allele> alleles, Map<String, Genotype> genotypes, Collection<Allele> alleles, Map<String, Genotype> genotypes,
double negLog10PError, Set<String> filters, Map<String, ?> attributes, double negLog10PError, Set<String> filters, Map<String, ?> attributes,
Byte referenceBaseForIndel, boolean genotypesAreUnparsed) { Byte referenceBaseForIndel, boolean genotypesAreUnparsed,
boolean performValidation ) {
if ( contig == null ) { throw new IllegalArgumentException("Contig cannot be null"); } if ( contig == null ) { throw new IllegalArgumentException("Contig cannot be null"); }
this.contig = contig; this.contig = contig;
this.start = start; this.start = start;
@ -371,39 +373,57 @@ public class VariantContext implements Feature { // to enable tribble intergrati
} }
} }
if ( performValidation ) {
validate(); validate();
} }
}
// --------------------------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------------------------
// //
// Partial-cloning routines (because Variant Context is immutable). // Partial-cloning routines (because Variant Context is immutable).
//
// IMPORTANT: These routines assume that the VariantContext on which they're called is already valid.
// Due to this assumption, they explicitly tell the constructor NOT to perform validation by
// calling validate(), and instead perform validation only on the data that's changed.
//
// Note that we don't call vc.getGenotypes() because that triggers the lazy loading. // Note that we don't call vc.getGenotypes() because that triggers the lazy loading.
// Also note that we need to create a new attributes map because it's unmodifiable and the constructor may try to modify it. // Also note that we need to create a new attributes map because it's unmodifiable and the constructor may try to modify it.
// //
// --------------------------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------------------------
public static VariantContext modifyGenotypes(VariantContext vc, Map<String, Genotype> genotypes) { public static VariantContext modifyGenotypes(VariantContext vc, Map<String, Genotype> genotypes) {
return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, new HashMap<String, Object>(vc.getAttributes()), vc.getReferenceBaseForIndel(), false); VariantContext modifiedVC = new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, new HashMap<String, Object>(vc.getAttributes()), vc.getReferenceBaseForIndel(), false, false);
modifiedVC.validateGenotypes();
return modifiedVC;
} }
public static VariantContext modifyLocation(VariantContext vc, String chr, int start, int end) { public static VariantContext modifyLocation(VariantContext vc, String chr, int start, int end) {
return new VariantContext(vc.getSource(), chr, start, end, vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, new HashMap<String, Object>(vc.getAttributes()), vc.getReferenceBaseForIndel(), true); VariantContext modifiedVC = new VariantContext(vc.getSource(), chr, start, end, vc.getAlleles(), vc.genotypes, vc.getNegLog10PError(), vc.filtersWereApplied() ? vc.getFilters() : null, new HashMap<String, Object>(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:
modifiedVC.validateAlleles();
modifiedVC.validateReferencePadding();
return modifiedVC;
} }
public static VariantContext modifyFilters(VariantContext vc, Set<String> filters) { 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); 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);
} }
public static VariantContext modifyAttributes(VariantContext vc, Map<String, Object> attributes) { 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); 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);
} }
public static VariantContext modifyReferencePadding(VariantContext vc, Byte b) { public static VariantContext modifyReferencePadding(VariantContext vc, Byte b) {
return 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); 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);
modifiedVC.validateReferencePadding();
return modifiedVC;
} }
public static VariantContext modifyPErrorFiltersAndAttributes(VariantContext vc, double negLog10PError, Set<String> filters, Map<String, Object> attributes) { 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); return new VariantContext(vc.getSource(), vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.genotypes, negLog10PError, filters, attributes, vc.getReferenceBaseForIndel(), true, false);
} }
// --------------------------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------------------------