List of usage examples for java.util LinkedHashSet add
boolean add(E e);
From source file:org.apache.hive.ptest.execution.conf.UnitTestPropertiesParser.java
private void addTestToResult(Map<String, LinkedHashSet<TestInfo>> result, TestInfo testInfo) { LinkedHashSet<TestInfo> moduleSet = result.get(testInfo.moduleName); if (moduleSet == null) { moduleSet = new LinkedHashSet<>(); result.put(testInfo.moduleName, moduleSet); }/*ww w . java 2 s. c om*/ moduleSet.add(testInfo); }
From source file:org.overlord.sramp.server.mvn.services.MavenFacadeServlet.java
/** * Generates the maven-metadata.xml file dynamically for a given groupId/artifactId pair. This will * list all of the versions available for that groupId+artifactId, along with the latest release and * snapshot versions.//from www. j a v a 2 s. co m * @param gavInfo */ private String doGenerateArtifactDirMavenMetaData(MavenGavInfo gavInfo) throws Exception { List<BaseArtifactType> artifacts = queryService.query("/s-ramp[@maven.groupId = '" + gavInfo.getGroupId() + "' and @maven.artifactId = '" + gavInfo.getArtifactId() + "']", "createdTimestamp", true); if (artifacts.size() == 0) { return null; } String groupId = gavInfo.getGroupId(); String artifactId = gavInfo.getArtifactId(); String latest = null; String release = null; String lastUpdated = null; LinkedHashSet<String> versions = new LinkedHashSet<String>(); SimpleDateFormat format = new SimpleDateFormat("yyyyMMddHHmmss"); for (BaseArtifactType artifact : artifacts) { String version = SrampModelUtils.getCustomProperty(artifact, "maven.version"); if (versions.add(version)) { latest = version; if (!version.endsWith("-SNAPSHOT")) { release = version; } } lastUpdated = format.format(artifact.getCreatedTimestamp().toGregorianCalendar().getTime()); } StringBuilder mavenMetadata = new StringBuilder(); mavenMetadata.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>"); mavenMetadata.append("<metadata>\n"); mavenMetadata.append(" <groupId>").append(groupId).append("</groupId>\n"); mavenMetadata.append(" <artifactId>").append(artifactId).append("</artifactId>\n"); mavenMetadata.append(" <versioning>\n"); mavenMetadata.append(" <latest>").append(latest).append("</latest>\n"); mavenMetadata.append(" <release>").append(release).append("</release>\n"); mavenMetadata.append(" <versions>\n"); for (String version : versions) { mavenMetadata.append(" <version>").append(version).append("</version>\n"); } mavenMetadata.append(" </versions>\n"); mavenMetadata.append(" <lastUpdated>").append(lastUpdated).append("</lastUpdated>\n"); mavenMetadata.append(" </versioning>\n"); mavenMetadata.append("</metadata>\n"); if (!gavInfo.isHash()) { return mavenMetadata.toString(); } else { return generateHash(mavenMetadata.toString(), gavInfo.getHashAlgorithm()); } }
From source file:org.apache.hadoop.yarn.server.resourcemanager.monitor.capacity.ProportionalCapacityPreemptionPolicy.java
public void addPartitionToUnderServedQueues(String queueName, String partition) { LinkedHashSet<String> underServedQueues = partitionToUnderServedQueues.get(partition); if (null == underServedQueues) { underServedQueues = new LinkedHashSet<String>(); partitionToUnderServedQueues.put(partition, underServedQueues); }/*from w w w. j av a2 s . com*/ underServedQueues.add(queueName); }
From source file:cz.incad.kramerius.pdf.impl.FirstPagePDFServiceImpl.java
String templateSelection(PreparedDocument rdoc, String... pids)
throws XPathExpressionException, IOException, ParserConfigurationException, SAXException {
ResourceBundle resourceBundle = resourceBundleService.getResourceBundle("base", localesProvider.get());
StringTemplate template = new StringTemplate(IOUtils.readAsString(
this.getClass().getResourceAsStream("templates/_first_page.st"), Charset.forName("UTF-8"), true));
FirstPageViewObject fpvo = prepareViewObject(resourceBundle);
// tistena polozka
GeneratedItem itm = new GeneratedItem();
Map<String, LinkedHashSet<String>> detailItemValues = new HashMap<String, LinkedHashSet<String>>();
Map<String, ObjectPidsPath> pathsMapping = new HashMap<String, ObjectPidsPath>();
LinkedHashSet<String> roots = new LinkedHashSet<String>();
for (String pid : pids) {
ObjectPidsPath sPath = selectOnePath(pid);
pathsMapping.put(pid, sPath);//from w ww .j a v a 2 s. co m
roots.add(sPath.getRoot());
}
for (String pid : pids) {
ObjectPidsPath path = pathsMapping.get(pid);
Map<String, Map<String, List<String>>> mods = processModsFromPath(path, null);
String rootPid = path.getRoot();
if (mods.get(rootPid).containsKey(TitleBuilder.MODS_TITLE)) {
List<String> list = mods.get(rootPid).get(TitleBuilder.MODS_TITLE);
if (!list.isEmpty()) {
String key = TitleBuilder.MODS_TITLE;
itemVals(detailItemValues, list, key);
}
}
String[] rProps = renderedProperties(roots.size() == 1);
String[] fromRootToLeaf = path.getPathFromRootToLeaf();
for (int i = 0; i < fromRootToLeaf.length; i++) {
String pidPath = fromRootToLeaf[i];
for (String prop : rProps) {
if (mods.get(pidPath).containsKey(prop)) {
List<String> list = mods.get(pidPath).get(prop);
itemVals(detailItemValues, list, prop);
}
}
}
}
// hlavni nazev
List<DetailItem> details = new ArrayList<FirstPagePDFServiceImpl.DetailItem>();
LinkedHashSet<String> maintitles = detailItemValues.get(TitleBuilder.MODS_TITLE);
String key = maintitles != null && maintitles.size() > 1 ? resourceBundle.getString("pdf.fp.titles")
: resourceBundle.getString("pdf.fp.title");
if (maintitles != null && (!maintitles.isEmpty())) {
details.add(new DetailItem(key, vals(maintitles).toString()));
}
for (String prop : renderedProperties(roots.size() == 1)) {
LinkedHashSet<String> vals = detailItemValues.get(prop);
key = vals != null && vals.size() > 1 ? resourceBundle.getString(i18nKey(prop) + "s")
: resourceBundle.getString(i18nKey(prop));
if (vals != null && (!vals.isEmpty())) {
details.add(new DetailItem(key, vals(vals).toString()));
}
}
// stranky v pdfku
pagesInSelectiontPdf(rdoc, resourceBundle, details);
itm.setDetailItems((DetailItem[]) details.toArray(new DetailItem[details.size()]));
fpvo.setGeneratedItems(new GeneratedItem[] { itm });
template.setAttribute("viewinfo", fpvo);
String templateText = template.toString();
return templateText;
}
From source file:com.streamsets.datacollector.definition.ConfigDefinitionExtractor.java
void resolveDependencies(String configPrefix, List<ConfigDefinition> defs, Object contextMsg) { Map<String, ConfigDefinition> definitionsMap = new HashMap<>(); Map<String, Map<String, Set<Object>>> dependencyMap = new HashMap<>(); Map<String, Boolean> isFullyProcessed = new HashMap<>(); for (ConfigDefinition def : defs) { definitionsMap.put(def.getName(), def); dependencyMap.put(def.getName(), new HashMap<String, Set<Object>>()); isFullyProcessed.put(def.getName(), false); }/*w w w.java2 s . c o m*/ cycles.clear(); for (ConfigDefinition def : defs) { String dependsOnKey = def.getDependsOn(); if (!StringUtils.isEmpty(dependsOnKey)) { verifyDependencyExists(definitionsMap, def, dependsOnKey, contextMsg); ConfigDefinition dependsOnDef = definitionsMap.get(dependsOnKey); // evaluate dependsOn triggers ConfigDef annotation = def.getConfigField().getAnnotation(ConfigDef.class); Set<Object> triggers = new HashSet<>(); for (String trigger : annotation.triggeredByValue()) { triggers.add(ConfigValueExtractor.get().extract(dependsOnDef.getConfigField(), dependsOnDef.getType(), trigger, contextMsg, true)); } dependencyMap.get(def.getName()).put(dependsOnDef.getName(), triggers); } // Add direct dependencies to dependencyMap if (!def.getDependsOnMap().isEmpty()) { // Copy same as above. for (Map.Entry<String, List<Object>> dependsOn : def.getDependsOnMap().entrySet()) { dependsOnKey = dependsOn.getKey(); if (!StringUtils.isEmpty(dependsOnKey)) { verifyDependencyExists(definitionsMap, def, dependsOnKey, contextMsg); Set<Object> triggers = new HashSet<>(); ConfigDefinition dependsOnDef = definitionsMap.get(dependsOnKey); for (Object trigger : dependsOn.getValue()) { triggers.add(ConfigValueExtractor.get().extract(dependsOnDef.getConfigField(), dependsOnDef.getType(), (String) trigger, contextMsg, true)); } Map<String, Set<Object>> dependencies = dependencyMap.get(def.getName()); if (dependencies.containsKey(dependsOnKey)) { dependencies.get(dependsOnKey).addAll(triggers); } else { dependencies.put(dependsOnKey, triggers); } } } } } for (ConfigDefinition def : defs) { if (isFullyProcessed.get(def.getName())) { continue; } // Now find all indirect dependencies Deque<StackNode> stack = new ArrayDeque<>(); stack.push(new StackNode(def, new LinkedHashSet<String>())); while (!stack.isEmpty()) { StackNode current = stack.peek(); // We processed this one's dependencies before, don't bother adding its children // The dependencies of this one have all been processed if (current.childrenAddedToStack) { stack.pop(); Map<String, Set<Object>> currentDependencies = dependencyMap.get(current.def.getName()); Set<String> children = new HashSet<>(current.def.getDependsOnMap().keySet()); for (String child : children) { if (StringUtils.isEmpty(child)) { continue; } Map<String, Set<Object>> depsOfChild = dependencyMap.get(child); for (Map.Entry<String, Set<Object>> depOfChild : depsOfChild.entrySet()) { if (currentDependencies.containsKey(depOfChild.getKey())) { // Add only the common trigger values, // since it has to be one of those for both these to be triggered. Set<Object> currentTriggers = currentDependencies.get(depOfChild.getKey()); Set<Object> childTriggers = depOfChild.getValue(); currentDependencies.put(depOfChild.getKey(), Sets.intersection(currentTriggers, childTriggers)); } else { currentDependencies.put(depOfChild.getKey(), new HashSet<>(depOfChild.getValue())); } } } isFullyProcessed.put(current.def.getName(), true); } else { Set<String> children = current.def.getDependsOnMap().keySet(); String dependsOn = current.def.getDependsOn(); LinkedHashSet<String> dependencyAncestors = new LinkedHashSet<>(current.ancestors); dependencyAncestors.add(current.def.getName()); if (!StringUtils.isEmpty(dependsOn) && !isFullyProcessed.get(current.def.getDependsOn()) && !detectCycle(dependencyAncestors, cycles, dependsOn)) { stack.push( new StackNode(definitionsMap.get(current.def.getDependsOn()), dependencyAncestors)); } for (String child : children) { if (!StringUtils.isEmpty(child) && !isFullyProcessed.get(child) && !detectCycle(dependencyAncestors, cycles, child)) { stack.push(new StackNode(definitionsMap.get(child), dependencyAncestors)); } } current.childrenAddedToStack = true; } } } Preconditions.checkState(cycles.isEmpty(), "The following cycles were detected in the configuration dependencies:\n" + Joiner.on("\n").join(cycles)); for (Map.Entry<String, Map<String, Set<Object>>> entry : dependencyMap.entrySet()) { Map<String, List<Object>> dependencies = new HashMap<>(); definitionsMap.get(entry.getKey()).setDependsOnMap(dependencies); for (Map.Entry<String, Set<Object>> trigger : entry.getValue().entrySet()) { List<Object> triggerValues = new ArrayList<>(); triggerValues.addAll(trigger.getValue()); dependencies.put(trigger.getKey(), triggerValues); } definitionsMap.get(entry.getKey()).setDependsOn(""); } }
From source file:de.andreasschoknecht.LS3.DocumentCollection.java
/** * Delete a model from the Term-Document Matrix search structure. * * @param modelName The model name of the model to be removed. *//*from w w w . j a v a 2s. c om*/ public void deleteModel(String modelName) { // Make sure file name is correct if (!modelName.endsWith(".pnml")) modelName = modelName + ".pnml"; // Delete column from TD Matrix and set correct number of columns int deletionIndex = 0; for (int i = 0, l = fileList.length; i < l; i++) { if (fileList[i].equals(modelName)) { tdMatrix.deleteColumn(i); deletionIndex = i; } } // Delete model name from fileList (update to new file list). String[] newFileList = new String[fileList.length - 1]; int counter = 0; for (int i = 0, l = fileList.length; i < l; i++) { if (i != deletionIndex) { newFileList[counter] = fileList[i]; counter++; } } setFileList(newFileList); // Delete LS3Document representation of file "modelName" (update to new ArrayList of LS3Documents). for (int i = 0, l = ls3Documents.size(); i < l; i++) { if (ls3Documents.get(i).getPNMLPath().endsWith(modelName)) { ls3Documents.remove(i); i = l; } } // Delete term rows that only contain values 0.0. I.e. delete unnecessary terms. ArrayList<Integer> termDeletionIndices = new ArrayList<Integer>(); boolean delete = true; double[][] matrix = tdMatrix.getMatrix(); for (int i = 0, k = tdMatrix.getRowNumber(); i < k; i++) { for (int j = 0, l = tdMatrix.getColumnNumber(); j < l; j++) { if (matrix[i][j] != 0.0) { delete = false; j = l; } } if (delete == true) termDeletionIndices.add(i); else delete = true; } int deletionCounter = 0; for (int index : termDeletionIndices) { tdMatrix.deleteRow(index - deletionCounter); deletionCounter++; } // Update term list of document collection. deletionCounter = 0; LinkedHashSet<String> newTermList = new LinkedHashSet<String>(); for (String term : termCollection) { if (!termDeletionIndices.contains(deletionCounter)) newTermList.add(term); deletionCounter++; } setTermCollection(newTermList); // Update term list of TDMatrix object tdMatrix.setTermArray(termCollection.toArray(new String[0])); }
From source file:eionet.cr.web.action.HarvestSourcesActionBean.java
/** * * @return// ww w . j av a2s . co m * @throws DAOException */ public Resolution delete() throws DAOException { if (isUserLoggedIn()) { if (sourceUrl != null && !sourceUrl.isEmpty()) { // An authenticated user can delete sources he own. An // administrator can delete any source. // A priority source can not be deleted. The administrator must // first change it to a non-priority source, then delete it. LinkedHashSet<String> sourcesToDelete = new LinkedHashSet<String>(); LinkedHashSet<String> notOwnedSources = new LinkedHashSet<String>(); LinkedHashSet<String> prioritySources = new LinkedHashSet<String>(); LinkedHashSet<String> currentlyHarvested = new LinkedHashSet<String>(); for (String url : sourceUrl) { HarvestSourceDTO source = factory.getDao(HarvestSourceDAO.class).getHarvestSourceByUrl(url); if (source != null) { if (CurrentHarvests.contains(url)) { currentlyHarvested.add(url); } else { if (userCanDelete(source)) { sourcesToDelete.add(url); } else if (source.isPrioritySource()) { prioritySources.add(url); } else if (!getUserName().equals(source.getOwner())) { notOwnedSources.add(url); } } } } logger.debug("Deleting the following sources: " + sourcesToDelete); factory.getDao(HarvestSourceDAO.class).removeHarvestSources(sourcesToDelete); if (!sourcesToDelete.isEmpty()) { StringBuffer msg = new StringBuffer(); msg.append("The following sources were successfully removed from the system: <ul>"); for (String uri : sourcesToDelete) { msg.append("<li>").append(uri).append("</li>"); } msg.append("</ul>"); addSystemMessage(msg.toString()); } StringBuffer warnings = new StringBuffer(); if (!prioritySources.isEmpty()) { warnings.append( "The following sources could not be deleted, because they are priority sources: <ul>"); for (String url : prioritySources) { warnings.append("<li>").append(url).append("</li>"); } warnings.append("</ul>"); } if (!notOwnedSources.isEmpty()) { warnings.append( "The following sources could not be deleted, because you are not their owner: <ul>"); for (String url : notOwnedSources) { warnings.append("<li>").append(url).append("</li>"); } warnings.append("</ul>"); } if (!currentlyHarvested.isEmpty()) { warnings.append( "The following sources could not be deleted, because they are curently being harvested: <ul>"); for (String url : currentlyHarvested) { warnings.append("<li>").append(url).append("</li>"); } warnings.append("</ul>"); } if (warnings.length() > 0) { addWarningMessage(warnings.toString()); } } } else { addWarningMessage(getBundle().getString("not.logged.in")); } return search(); }
From source file:com.clust4j.utils.VecUtils.java
public static LinkedHashSet<Double> unique(final double[] arr) { final LinkedHashSet<Double> out = new LinkedHashSet<>(); for (Double t : arr) out.add(t); return out;/*from ww w . j a va2s . c om*/ }
From source file:com.clust4j.utils.VecUtils.java
public static LinkedHashSet<Integer> unique(final int[] arr) { final LinkedHashSet<Integer> out = new LinkedHashSet<>(); for (Integer t : arr) out.add(t); return out;/*from ww w . java 2s . com*/ }
From source file:org.broadinstitute.sting.utils.variant.GATKVariantContextUtils.java
/** * Merges VariantContexts into a single hybrid. Takes genotypes for common samples in priority order, if provided. * If uniquifySamples is true, the priority order is ignored and names are created by concatenating the VC name with * the sample name.//from ww w. j av a 2s .c o m * simpleMerge does not verify any more unique sample names EVEN if genotypeMergeOptions == GenotypeMergeType.REQUIRE_UNIQUE. One should use * SampleUtils.verifyUniqueSamplesNames to check that before using sempleMerge. * * For more information on this method see: http://www.thedistractionnetwork.com/programmer-problem/ * * @param unsortedVCs collection of unsorted VCs * @param priorityListOfVCs priority list detailing the order in which we should grab the VCs * @param filteredRecordMergeType merge type for filtered records * @param genotypeMergeOptions merge option for genotypes * @param annotateOrigin should we annotate the set it came from? * @param printMessages should we print messages? * @param setKey the key name of the set * @param filteredAreUncalled are filtered records uncalled? * @param mergeInfoWithMaxAC should we merge in info from the VC with maximum allele count? * @return new VariantContext representing the merge of unsortedVCs */ public static VariantContext simpleMerge(final Collection<VariantContext> unsortedVCs, final List<String> priorityListOfVCs, final int originalNumOfVCs, final FilteredRecordMergeType filteredRecordMergeType, final GenotypeMergeType genotypeMergeOptions, final boolean annotateOrigin, final boolean printMessages, final String setKey, final boolean filteredAreUncalled, final boolean mergeInfoWithMaxAC) { if (unsortedVCs == null || unsortedVCs.size() == 0) return null; if (priorityListOfVCs != null && originalNumOfVCs != priorityListOfVCs.size()) throw new IllegalArgumentException( "the number of the original VariantContexts must be the same as the number of VariantContexts in the priority list"); if (annotateOrigin && priorityListOfVCs == null && originalNumOfVCs == 0) throw new IllegalArgumentException( "Cannot merge calls and annotate their origins without a complete priority list of VariantContexts or the number of original VariantContexts"); final List<VariantContext> preFilteredVCs = sortVariantContextsByPriority(unsortedVCs, priorityListOfVCs, genotypeMergeOptions); // Make sure all variant contexts are padded with reference base in case of indels if necessary final List<VariantContext> VCs = new ArrayList<VariantContext>(); for (final VariantContext vc : preFilteredVCs) { if (!filteredAreUncalled || vc.isNotFiltered()) VCs.add(vc); } if (VCs.size() == 0) // everything is filtered out and we're filteredAreUncalled return null; // establish the baseline info from the first VC final VariantContext first = VCs.get(0); final String name = first.getSource(); final Allele refAllele = determineReferenceAllele(VCs); final Set<Allele> alleles = new LinkedHashSet<Allele>(); final Set<String> filters = new HashSet<String>(); final Map<String, Object> attributes = new LinkedHashMap<String, Object>(); final Set<String> inconsistentAttributes = new HashSet<String>(); final Set<String> variantSources = new HashSet<String>(); // contains the set of sources we found in our set of VCs that are variant final Set<String> rsIDs = new LinkedHashSet<String>(1); // most of the time there's one id VariantContext longestVC = first; int depth = 0; int maxAC = -1; final Map<String, Object> attributesWithMaxAC = new LinkedHashMap<String, Object>(); double log10PError = CommonInfo.NO_LOG10_PERROR; VariantContext vcWithMaxAC = null; GenotypesContext genotypes = GenotypesContext.create(); // counting the number of filtered and variant VCs int nFiltered = 0; boolean remapped = false; // cycle through and add info from the other VCs, making sure the loc/reference matches for (final VariantContext vc : VCs) { if (longestVC.getStart() != vc.getStart()) throw new IllegalStateException( "BUG: attempting to merge VariantContexts with different start sites: first=" + first.toString() + " second=" + vc.toString()); if (VariantContextUtils.getSize(vc) > VariantContextUtils.getSize(longestVC)) longestVC = vc; // get the longest location nFiltered += vc.isFiltered() ? 1 : 0; if (vc.isVariant()) variantSources.add(vc.getSource()); AlleleMapper alleleMapping = resolveIncompatibleAlleles(refAllele, vc, alleles); remapped = remapped || alleleMapping.needsRemapping(); alleles.addAll(alleleMapping.values()); mergeGenotypes(genotypes, vc, alleleMapping, genotypeMergeOptions == GenotypeMergeType.UNIQUIFY); // We always take the QUAL of the first VC with a non-MISSING qual for the combined value if (log10PError == CommonInfo.NO_LOG10_PERROR) log10PError = vc.getLog10PError(); filters.addAll(vc.getFilters()); // // add attributes // // special case DP (add it up) and ID (just preserve it) // if (vc.hasAttribute(VCFConstants.DEPTH_KEY)) depth += vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0); if (vc.hasID()) rsIDs.add(vc.getID()); if (mergeInfoWithMaxAC && vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) { String rawAlleleCounts = vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY, null); // lets see if the string contains a , separator if (rawAlleleCounts.contains(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR)) { List<String> alleleCountArray = Arrays .asList(rawAlleleCounts.substring(1, rawAlleleCounts.length() - 1) .split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR)); for (String alleleCount : alleleCountArray) { final int ac = Integer.valueOf(alleleCount.trim()); if (ac > maxAC) { maxAC = ac; vcWithMaxAC = vc; } } } else { final int ac = Integer.valueOf(rawAlleleCounts); if (ac > maxAC) { maxAC = ac; vcWithMaxAC = vc; } } } for (final Map.Entry<String, Object> p : vc.getAttributes().entrySet()) { String key = p.getKey(); // if we don't like the key already, don't go anywhere if (!inconsistentAttributes.contains(key)) { final boolean alreadyFound = attributes.containsKey(key); final Object boundValue = attributes.get(key); final boolean boundIsMissingValue = alreadyFound && boundValue.equals(VCFConstants.MISSING_VALUE_v4); if (alreadyFound && !boundValue.equals(p.getValue()) && !boundIsMissingValue) { // we found the value but we're inconsistent, put it in the exclude list //System.out.printf("Inconsistent INFO values: %s => %s and %s%n", key, boundValue, p.getValue()); inconsistentAttributes.add(key); attributes.remove(key); } else if (!alreadyFound || boundIsMissingValue) { // no value //if ( vc != first ) System.out.printf("Adding key %s => %s%n", p.getKey(), p.getValue()); attributes.put(key, p.getValue()); } } } } // if we have more alternate alleles in the merged VC than in one or more of the // original VCs, we need to strip out the GL/PLs (because they are no longer accurate), as well as allele-dependent attributes like AC,AF, and AD for (final VariantContext vc : VCs) { if (vc.getAlleles().size() == 1) continue; if (hasPLIncompatibleAlleles(alleles, vc.getAlleles())) { if (!genotypes.isEmpty()) { logger.debug(String.format( "Stripping PLs at %s:%d-%d due to incompatible alleles merged=%s vs. single=%s", vc.getChr(), vc.getStart(), vc.getEnd(), alleles, vc.getAlleles())); } genotypes = stripPLsAndAD(genotypes); // this will remove stale AC,AF attributed from vc VariantContextUtils.calculateChromosomeCounts(vc, attributes, true); break; } } // take the VC with the maxAC and pull the attributes into a modifiable map if (mergeInfoWithMaxAC && vcWithMaxAC != null) { attributesWithMaxAC.putAll(vcWithMaxAC.getAttributes()); } // if at least one record was unfiltered and we want a union, clear all of the filters if ((filteredRecordMergeType == FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED && nFiltered != VCs.size()) || filteredRecordMergeType == FilteredRecordMergeType.KEEP_UNCONDITIONAL) filters.clear(); if (annotateOrigin) { // we care about where the call came from String setValue; if (nFiltered == 0 && variantSources.size() == originalNumOfVCs) // nothing was unfiltered setValue = MERGE_INTERSECTION; else if (nFiltered == VCs.size()) // everything was filtered out setValue = MERGE_FILTER_IN_ALL; else if (variantSources.isEmpty()) // everyone was reference setValue = MERGE_REF_IN_ALL; else { final LinkedHashSet<String> s = new LinkedHashSet<String>(); for (final VariantContext vc : VCs) if (vc.isVariant()) s.add(vc.isFiltered() ? MERGE_FILTER_PREFIX + vc.getSource() : vc.getSource()); setValue = Utils.join("-", s); } if (setKey != null) { attributes.put(setKey, setValue); if (mergeInfoWithMaxAC && vcWithMaxAC != null) { attributesWithMaxAC.put(setKey, setValue); } } } if (depth > 0) attributes.put(VCFConstants.DEPTH_KEY, String.valueOf(depth)); final String ID = rsIDs.isEmpty() ? VCFConstants.EMPTY_ID_FIELD : Utils.join(",", rsIDs); final VariantContextBuilder builder = new VariantContextBuilder().source(name).id(ID); builder.loc(longestVC.getChr(), longestVC.getStart(), longestVC.getEnd()); builder.alleles(alleles); builder.genotypes(genotypes); builder.log10PError(log10PError); builder.filters(filters.isEmpty() ? filters : new TreeSet<String>(filters)); builder.attributes(new TreeMap<String, Object>(mergeInfoWithMaxAC ? attributesWithMaxAC : attributes)); // Trim the padded bases of all alleles if necessary final VariantContext merged = builder.make(); if (printMessages && remapped) System.out.printf("Remapped => %s%n", merged); return merged; }