Bug fixes and code cleanup throughout
-- chromosomeCounts now takes builder as well, cleaning up a lot of code throughout the codebase.
This commit is contained in:
Mark DePristo
parent
707bd30b3f
commit
7d09c0064b
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@ -59,10 +59,8 @@ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnn
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public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
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if ( ! vc.hasGenotypes() )
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return null;
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Map<String, Object> map = new HashMap<String, Object>();
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VariantContextUtils.calculateChromosomeCounts(vc, map, true);
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return map;
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return VariantContextUtils.calculateChromosomeCounts(vc, new HashMap<String, Object>(), true);
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}
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public List<String> getKeyNames() {
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@ -338,23 +338,21 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
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builder.alleles(new HashSet<Allele>(Arrays.asList(vc_input.getReference()))).filters(removedFilters);
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}
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HashMap<String, Object> attributes = new HashMap<String, Object>(vc_input.getAttributes());
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// re-compute chromosome counts
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VariantContextUtils.calculateChromosomeCounts(vc_input, attributes, false);
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VariantContextUtils.calculateChromosomeCounts(builder, false);
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// Get Hapmap AC and AF
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if (vc_comp != null) {
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attributes.put("ACH", alleleCountH.toString() );
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attributes.put("ANH", chrCountH.toString() );
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attributes.put("AFH", String.format("%4.2f", (double)alleleCountH/chrCountH) );
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builder.attribute("ACH", alleleCountH.toString() );
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builder.attribute("ANH", chrCountH.toString() );
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builder.attribute("AFH", String.format("%4.2f", (double)alleleCountH/chrCountH) );
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}
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attributes.put("NumGenotypesChanged", numGenotypesChangedByBeagle );
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builder.attribute("NumGenotypesChanged", numGenotypesChangedByBeagle );
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if( !beagleR2Feature.getR2value().equals(Double.NaN) ) {
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attributes.put("R2", beagleR2Feature.getR2value().toString() );
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builder.attribute("R2", beagleR2Feature.getR2value().toString() );
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}
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builder.attributes(attributes);
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vcfWriter.add(builder.make());
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@ -106,9 +106,9 @@ public class UGCallVariants extends RodWalker<VariantCallContext, Integer> {
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return sum;
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try {
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Map<String, Object> attrs = new HashMap<String, Object>(value.getAttributes());
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VariantContextUtils.calculateChromosomeCounts(value, attrs, true);
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writer.add(new VariantContextBuilder(value).attributes(attrs).make());
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VariantContextBuilder builder = new VariantContextBuilder(value);
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VariantContextUtils.calculateChromosomeCounts(builder, true);
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writer.add(builder.make());
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} catch (IllegalArgumentException e) {
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throw new IllegalArgumentException(e.getMessage() + "; this is often caused by using the --assume_single_sample_reads argument with the wrong sample name");
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}
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@ -131,13 +131,9 @@ class PhasingUtils {
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if ( vc2.hasID() ) mergedIDs.add(vc2.getID());
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String mergedID = mergedIDs.isEmpty() ? VCFConstants.EMPTY_ID_FIELD : Utils.join(VCFConstants.ID_FIELD_SEPARATOR, mergedIDs);
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VariantContext mergedVc = new VariantContextBuilder(mergedName, vc1.getChr(), vc1.getStart(), vc2.getEnd(), mergeData.getAllMergedAlleles()).id(mergedID).genotypes(mergedGenotypes).log10PError(mergedLog10PError).filters(mergedFilters).attributes(mergedAttribs).make();
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mergedAttribs = new HashMap<String, Object>(mergedVc.getAttributes());
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VariantContextUtils.calculateChromosomeCounts(mergedVc, mergedAttribs, true);
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mergedVc = new VariantContextBuilder(mergedVc).attributes(mergedAttribs).make();
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return mergedVc;
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VariantContextBuilder mergedBuilder = new VariantContextBuilder(mergedName, vc1.getChr(), vc1.getStart(), vc2.getEnd(), mergeData.getAllMergedAlleles()).id(mergedID).genotypes(mergedGenotypes).log10PError(mergedLog10PError).filters(mergedFilters).attributes(mergedAttribs);
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VariantContextUtils.calculateChromosomeCounts(mergedBuilder, true);
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return mergedBuilder.make();
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}
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static String mergeVariantContextNames(String name1, String name2) {
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@ -279,22 +279,17 @@ public class VariantEvalUtils {
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*/
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public VariantContext getSubsetOfVariantContext(VariantContext vc, Set<String> sampleNames) {
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VariantContext vcsub = vc.subContextFromSamples(sampleNames, vc.getAlleles());
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VariantContextBuilder builder = new VariantContextBuilder(vcsub);
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HashMap<String, Object> newAts = new HashMap<String, Object>(vcsub.getAttributes());
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int originalAlleleCount = vc.getHetCount() + 2 * vc.getHomVarCount();
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int newAlleleCount = vcsub.getHetCount() + 2 * vcsub.getHomVarCount();
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final int originalAlleleCount = vc.getHetCount() + 2 * vc.getHomVarCount();
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final int newAlleleCount = vcsub.getHetCount() + 2 * vcsub.getHomVarCount();
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if (originalAlleleCount == newAlleleCount && newAlleleCount == 1) {
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newAts.put("ISSINGLETON", true);
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builder.attribute("ISSINGLETON", true);
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}
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VariantContextUtils.calculateChromosomeCounts(vcsub, newAts, true);
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vcsub = new VariantContextBuilder(vcsub).attributes(newAts).make();
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//VariantEvalWalker.logger.debug(String.format("VC %s subset to %s AC%n", vc.getSource(), vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY)));
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return vcsub;
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VariantContextUtils.calculateChromosomeCounts(builder, true);
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return builder.make();
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}
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/**
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@ -222,7 +222,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
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for ( final VariantContext vc : vcs ) {
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vcfWriter.add(vc);
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}
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return vcs.isEmpty() ? 0 : 1;
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}
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@ -245,18 +245,17 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
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SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC));
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}
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for ( VariantContext mergedVC : mergedVCs ) {
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for ( VariantContext mergedVC : mergedVCs ) {
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// only operate at the start of events
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if ( mergedVC == null )
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continue;
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HashMap<String, Object> attributes = new HashMap<String, Object>(mergedVC.getAttributes());
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final VariantContextBuilder builder = new VariantContextBuilder(mergedVC);
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// re-compute chromosome counts
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VariantContextUtils.calculateChromosomeCounts(mergedVC, attributes, false);
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VariantContext annotatedMergedVC = new VariantContextBuilder(mergedVC).attributes(attributes).make();
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VariantContextUtils.calculateChromosomeCounts(builder, false);
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if ( minimalVCF )
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annotatedMergedVC = VariantContextUtils.pruneVariantContext(annotatedMergedVC, Arrays.asList(SET_KEY));
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vcfWriter.add(annotatedMergedVC);
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VariantContextUtils.pruneVariantContext(builder, Arrays.asList(SET_KEY));
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vcfWriter.add(builder.make());
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}
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return vcs.isEmpty() ? 0 : 1;
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@ -684,11 +684,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
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builder.attribute("AN_Orig", sub.getAttribute(VCFConstants.ALLELE_NUMBER_KEY));
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}
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Map<String, Object> attributes = new HashMap<String, Object>(builder.make().getAttributes());
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VariantContextUtils.calculateChromosomeCounts(sub, attributes, false);
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attributes.put("DP", depth);
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VariantContextUtils.calculateChromosomeCounts(builder, false);
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builder.attribute("DP", depth);
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return new VariantContextBuilder(builder.make()).attributes(attributes).make();
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return builder.make();
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}
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private void randomlyAddVariant(int rank, VariantContext vc) {
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@ -158,12 +158,34 @@ public class VariantContextBuilder {
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@Requires({"key != null"})
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@Ensures({"this.attributes.size() == old(this.attributes.size()) || this.attributes.size() == old(this.attributes.size()+1)"})
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public VariantContextBuilder attribute(final String key, final Object value) {
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makeAttributesModifiable();
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attributes.put(key, value);
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return this;
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}
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/**
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* Removes key if present in the attributes
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*
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* @param key
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* @return
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*/
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@Requires({"key != null"})
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@Ensures({"this.attributes.size() == old(this.attributes.size()) || this.attributes.size() == old(this.attributes.size()-1)"})
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public VariantContextBuilder rmAttribute(final String key) {
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makeAttributesModifiable();
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attributes.remove(key);
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return this;
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}
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/**
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* Makes the attributes field modifiable. In many cases attributes is just a pointer to an immutable
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* collection, so methods that want to add / remove records require the attributes to be copied first
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*/
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private void makeAttributesModifiable() {
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if ( ! attributesCanBeModified ) {
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this.attributesCanBeModified = true;
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this.attributes = new HashMap<String, Object>(attributes);
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}
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attributes.put(key, value);
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return this;
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}
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/**
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@ -55,13 +55,15 @@ public class VariantContextUtils {
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}
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/**
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* Update the attributes of the attributes map given the VariantContext to reflect the proper chromosome-based VCF tags
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* Update the attributes of the attributes map given the VariantContext to reflect the
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* proper chromosome-based VCF tags
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*
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* @param vc the VariantContext
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* @param attributes the attributes map to populate; must not be null; may contain old values
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* @param removeStaleValues should we remove stale values from the mapping?
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* @return the attributes map provided as input, returned for programming convenience
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*/
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public static void calculateChromosomeCounts(VariantContext vc, Map<String, Object> attributes, boolean removeStaleValues) {
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public static Map<String, Object> calculateChromosomeCounts(VariantContext vc, Map<String, Object> attributes, boolean removeStaleValues) {
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// if everyone is a no-call, remove the old attributes if requested
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if ( vc.getCalledChrCount() == 0 && removeStaleValues ) {
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if ( attributes.containsKey(VCFConstants.ALLELE_COUNT_KEY) )
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@ -70,7 +72,7 @@ public class VariantContextUtils {
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attributes.remove(VCFConstants.ALLELE_FREQUENCY_KEY);
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if ( attributes.containsKey(VCFConstants.ALLELE_NUMBER_KEY) )
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attributes.remove(VCFConstants.ALLELE_NUMBER_KEY);
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return;
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return attributes;
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}
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if ( vc.hasGenotypes() ) {
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@ -96,6 +98,54 @@ public class VariantContextUtils {
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attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, 0.0);
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}
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}
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return attributes;
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}
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/**
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* Update the attributes of the attributes map in the VariantContextBuilder to reflect the proper
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* chromosome-based VCF tags based on the current VC produced by builder.make()
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*
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* @param builder the VariantContextBuilder we are updating
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* @param removeStaleValues should we remove stale values from the mapping?
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*/
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public static void calculateChromosomeCounts(VariantContextBuilder builder, boolean removeStaleValues) {
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final VariantContext vc = builder.make();
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// if everyone is a no-call, remove the old attributes if requested
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if ( vc.getCalledChrCount() == 0 && removeStaleValues ) {
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if ( vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY) )
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builder.rmAttribute(VCFConstants.ALLELE_COUNT_KEY);
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if ( vc.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) )
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builder.rmAttribute(VCFConstants.ALLELE_FREQUENCY_KEY);
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if ( vc.hasAttribute(VCFConstants.ALLELE_NUMBER_KEY) )
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builder.rmAttribute(VCFConstants.ALLELE_NUMBER_KEY);
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return;
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}
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if ( vc.hasGenotypes() ) {
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builder.attribute(VCFConstants.ALLELE_NUMBER_KEY, vc.getCalledChrCount());
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// if there are alternate alleles, record the relevant tags
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if ( vc.getAlternateAlleles().size() > 0 ) {
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ArrayList<String> alleleFreqs = new ArrayList<String>();
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ArrayList<Integer> alleleCounts = new ArrayList<Integer>();
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double totalChromosomes = (double)vc.getCalledChrCount();
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for ( Allele allele : vc.getAlternateAlleles() ) {
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int altChromosomes = vc.getCalledChrCount(allele);
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alleleCounts.add(altChromosomes);
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String freq = String.format(makePrecisionFormatStringFromDenominatorValue(totalChromosomes), ((double)altChromosomes / totalChromosomes));
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alleleFreqs.add(freq);
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}
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builder.attribute(VCFConstants.ALLELE_COUNT_KEY, alleleCounts.size() == 1 ? alleleCounts.get(0) : alleleCounts);
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builder.attribute(VCFConstants.ALLELE_FREQUENCY_KEY, alleleFreqs.size() == 1 ? alleleFreqs.get(0) : alleleFreqs);
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}
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else {
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builder.attribute(VCFConstants.ALLELE_COUNT_KEY, 0);
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builder.attribute(VCFConstants.ALLELE_FREQUENCY_KEY, 0.0);
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}
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}
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}
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private static String makePrecisionFormatStringFromDenominatorValue(double maxValue) {
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@ -348,10 +398,6 @@ public class VariantContextUtils {
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return r;
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}
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public static VariantContext pruneVariantContext(VariantContext vc) {
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return pruneVariantContext(vc, null);
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}
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private final static Map<String, Object> subsetAttributes(final CommonInfo igc, final Collection<String> keysToPreserve) {
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Map<String, Object> attributes = new HashMap<String, Object>(keysToPreserve.size());
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for ( final String key : keysToPreserve ) {
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@ -361,7 +407,19 @@ public class VariantContextUtils {
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return attributes;
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}
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/**
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* @deprecated use variant context builder version instead
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* @param vc
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* @param keysToPreserve
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* @return
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*/
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@Deprecated
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public static VariantContext pruneVariantContext(final VariantContext vc, Collection<String> keysToPreserve ) {
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return pruneVariantContext(new VariantContextBuilder(vc), keysToPreserve).make();
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}
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public static VariantContextBuilder pruneVariantContext(final VariantContextBuilder builder, Collection<String> keysToPreserve ) {
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final VariantContext vc = builder.make();
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if ( keysToPreserve == null ) keysToPreserve = Collections.emptyList();
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// VC info
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@ -375,7 +433,7 @@ public class VariantContextUtils {
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genotypeAttributes, g.isPhased()));
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}
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return new VariantContextBuilder(vc).genotypes(genotypes).attributes(attributes).make();
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return builder.genotypes(genotypes).attributes(attributes);
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}
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public enum GenotypeMergeType {
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@ -32,7 +32,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testHasAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("9beb795536e95954f810835c6058f2ad"));
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Arrays.asList("fbb656369eaa48153d127bd12db59d8f"));
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executeTest("test file has annotations, asking for annotations, #1", spec);
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}
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@ -54,9 +54,11 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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@Test
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public void testNoAnnotsNotAsking2() {
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// this genotype annotations in this file are actually out of order. If you don't parse the genotypes
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// they don't get reordered. It's a good test of the genotype ordering system.
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
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Arrays.asList("f2ddfa8105c290b1f34b7a261a02a1ac"));
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Arrays.asList("0cc0ec59f0328792e6413b6ff3f71780"));
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executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
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}
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@ -64,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testNoAnnotsAsking1() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("49d989f467b8d6d8f98f7c1b67cd4a05"));
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Arrays.asList("42dd979a0a931c18dc9be40308bac321"));
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executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
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}
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@ -80,7 +82,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
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public void testExcludeAnnotations() {
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WalkerTestSpec spec = new WalkerTestSpec(
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baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant:VCF3 " + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
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Arrays.asList("33062eccd6eb73bc49440365430454c4"));
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Arrays.asList("477eac07989593b58bb361f3429c085a"));
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executeTest("test exclude annotations", spec);
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}
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