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- Added flag to ease restrictions on b37 reference for chr/non-chr co…
…mparisons. This is useful for dev testing. - Added parsing of funcotation attribute using the VCF Header. Mostly used for dev testing. - VCF Datasources now have to match the alt and ref alleles to be condsidered a hit. - Fixing #4808 - Added FuncotationMap to improve encapsulation and make rendering a bit easier. - Fixed issue with FuncotatorIntegrationTest where default values were references that were changed, thereby causing cross-test errors. - A lot of refactoring to create FuncotationMap and use that to send to OutputRenderers. - VCF and MAF will honor the canonical vs. all vs best effect.
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208
src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotationMap.java
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| package org.broadinstitute.hellbender.tools.funcotator; | ||
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| import htsjdk.variant.variantcontext.Allele; | ||
| import org.apache.commons.lang3.StringUtils; | ||
| import org.apache.logging.log4j.LogManager; | ||
| import org.apache.logging.log4j.Logger; | ||
| import org.broadinstitute.hellbender.exceptions.GATKException; | ||
| import org.broadinstitute.hellbender.tools.funcotator.dataSources.TableFuncotation; | ||
| import org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.GencodeFuncotation; | ||
| import org.broadinstitute.hellbender.tools.funcotator.vcfOutput.VcfOutputRenderer; | ||
| import org.broadinstitute.hellbender.utils.Utils; | ||
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| import java.util.*; | ||
| import java.util.stream.Collectors; | ||
| import java.util.stream.IntStream; | ||
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| /** | ||
| * A linked map of transcript IDs to funcotations. Also, supports some querying. | ||
| * | ||
| * Supports ordering of the transcripts. | ||
| * | ||
| * Multiple GencodeFuncotations for the same transcript are prohibited. | ||
| * | ||
| * Not thread-safe. | ||
| */ | ||
| public class FuncotationMap { | ||
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| public final static String NO_TRANSCRIPT_AVAILABLE_KEY = "no_transcript"; | ||
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| /** Standard Logger. */ | ||
| protected static final Logger logger = LogManager.getLogger(FuncotationMap.class); | ||
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| final private Map<String, LinkedHashSet<Funcotation>> txToFuncotations = new LinkedHashMap<>(); | ||
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| private FuncotationMap() {} | ||
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| private static boolean isGencodeFuncotation(final Funcotation f) { | ||
| return f instanceof GencodeFuncotation; | ||
| } | ||
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| /** | ||
| * @param transcriptId the specified transcript ID. Use {@see NO_TRANSCRIPT_AVAILABLE_KEY} if there are no transcripts. Never {@code null} | ||
| * @return A list of the Gencode Funcotations only. Empty list, if nothing found. Never {@code null} | ||
| */ | ||
| public List<GencodeFuncotation> getGencodeFuncotations(final String transcriptId) { | ||
| Utils.nonNull(transcriptId); | ||
| return txToFuncotations.getOrDefault(transcriptId, new LinkedHashSet<>()).stream() | ||
| .filter(FuncotationMap::isGencodeFuncotation).map(f-> (GencodeFuncotation) f).collect(Collectors.toList()); | ||
| } | ||
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| /** | ||
| * Get all funcotations for the given transcript. Note that the alleles will be mixed. | ||
| * @param transcriptId the specified transcript ID. Use {@see NO_TRANSCRIPT_AVAILABLE_KEY} if there are no transcripts. | ||
| * @return Empty list, if nothing found. Never {@code null} | ||
| */ | ||
| public List<Funcotation> get(final String transcriptId) { | ||
| Utils.nonNull(transcriptId); | ||
| return new ArrayList<>(txToFuncotations.getOrDefault(transcriptId, new LinkedHashSet<>())); | ||
| } | ||
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| /** | ||
| * @param transcriptId the specified transcript ID. Use {@see NO_TRANSCRIPT_AVAILABLE_KEY} if there are no transcripts. Never {@code null} | ||
| * @param fieldName The field name to search. Never {@code null} | ||
| * @param allele Only return fields from funcotations with the specified allele. Never {@code null} | ||
| * @return Value of the given field for the transcript ID and allele. Return {@code null} if field not found. | ||
| */ | ||
| public String getFieldValue(final String transcriptId, final String fieldName, final Allele allele) { | ||
| Utils.nonNull(transcriptId); | ||
| Utils.nonNull(fieldName); | ||
| Utils.nonNull(allele); | ||
| final List<String> values = txToFuncotations.getOrDefault(transcriptId, new LinkedHashSet<>()).stream() | ||
| .filter(f -> f.hasField(fieldName)) | ||
| .filter(f -> f.getAltAllele().equals(allele)) | ||
| .map(f -> f.getField(fieldName)) | ||
| .collect(Collectors.toList()); | ||
| if (values.size() > 1) { | ||
| throw new GATKException.ShouldNeverReachHereException("Found more than one value for " + transcriptId + ", " | ||
| + allele + ", " + fieldName); | ||
| } | ||
| if (values.size() == 0) { | ||
| return null; | ||
| } else { | ||
| return values.get(0); | ||
| } | ||
| } | ||
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| /** | ||
| * @return An empty FuncotationMap. Never {@code null} | ||
| */ | ||
| private static FuncotationMap createEmpty() { | ||
| return new FuncotationMap(); | ||
| } | ||
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| /** | ||
| * @return A FuncotationMap with only one transcript ID, which is {@see NO_TRANSCRIPT_AVAILABLE_KEY}. Never {@code null} | ||
| */ | ||
| public static FuncotationMap createNoTranscriptInfo(final List<Funcotation> funcotations) { | ||
| final FuncotationMap result = createEmpty(); | ||
| result.add(NO_TRANSCRIPT_AVAILABLE_KEY, funcotations); | ||
| return result; | ||
| } | ||
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| /** This method checks for transcript duplications in the list of GencodeFuncotations. | ||
| * Recommended to gather all gencode funcotations before calling this method. | ||
| * @param gencodeFuncotations Never {@code null} | ||
| * @return A new FuncotationMap created only from the given list of GencodeFuncotations. Never {@code null} | ||
| */ | ||
| public static FuncotationMap createFromGencodeFuncotations(final List<GencodeFuncotation> gencodeFuncotations) { | ||
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| Utils.nonNull(gencodeFuncotations); | ||
| Utils.validateArg(!areDuplicateTranscriptIDsFound(gencodeFuncotations), "Duplicate transcript ID entries were found in input: " + | ||
| gencodeFuncotations.stream().map(gf -> gf.getAnnotationTranscript()).collect(Collectors.joining(","))); | ||
| final FuncotationMap result = createEmpty(); | ||
| gencodeFuncotations.forEach(f -> result.add(f.getAnnotationTranscript(), f)); | ||
| return result; | ||
| } | ||
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| /** | ||
| * Add the given funcotations to the given transcript ID. | ||
| * | ||
| * @param txId Never {@code null} | ||
| * @param funcotations Never {@code null} | ||
| */ | ||
| public void add(final String txId, final List<Funcotation> funcotations) { | ||
| Utils.nonNull(txId); | ||
| Utils.nonNull(funcotations); | ||
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| final LinkedHashSet<Funcotation> existingFuncotationsToUpdate = txToFuncotations.getOrDefault(txId, new LinkedHashSet<>()); | ||
| existingFuncotationsToUpdate.addAll(funcotations); | ||
| txToFuncotations.put(txId, existingFuncotationsToUpdate); | ||
| } | ||
| /** Add the given funcotation to the given transcript ID. | ||
| * | ||
| * @param txId Never {@code null} | ||
| * @param funcotation Never {@code null} | ||
| */ | ||
| public void add(final String txId, final Funcotation funcotation) { | ||
| Utils.nonNull(txId); | ||
| Utils.nonNull(funcotation); | ||
| final LinkedHashSet<Funcotation> existingFuncotationsToUpdate = txToFuncotations.getOrDefault(txId, new LinkedHashSet<>()); | ||
| existingFuncotationsToUpdate.add(funcotation); | ||
| txToFuncotations.put(txId, existingFuncotationsToUpdate); | ||
| } | ||
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| /** | ||
| * Get the key list (i.e. transcript IDs) in order. | ||
| * | ||
| * @return Never {@code null} | ||
| */ | ||
| public List<String> keyList() { | ||
| return new ArrayList<>(txToFuncotations.keySet()); | ||
| } | ||
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| /** Create a FuncotationMap where all Funcotations will be TableFuncotations. This is useful for parsing existing | ||
| * VCFs. | ||
| * Only renders for a single allele. | ||
| * See {@link FuncotatorUtils#extractFuncotatorKeysFromHeaderDescription(String)} for getting the funcotation keys. | ||
| * | ||
| * @param transcriptFieldName The field name to use for transcript IDs. Use {@see NO_TRANSCRIPT_AVAILABLE_KEY} if unknown. | ||
| * If not in the funcotation keys, then the Funcotation map will be created with one transcript ID, {@see NO_TRANSCRIPT_AVAILABLE_KEY} | ||
| * Never {@code null} | ||
| * @param funcotationKeys The ordered keys of the funcotation field. Never {@code null} | ||
| * @param funcotationAttributeForSingleAllele The funcotation attribute from a VCF. Never {@code null} | ||
| * @param altAllele The alternate allele for the created funcotations. Never {@code null} | ||
| * @param datasourceName The datasource name to use for all of the created funcotatinos. Never {@code null} | ||
| * @return a funcotation map. Note that no funcotations will be GencodeFuncotations. Never {@code null} | ||
| */ | ||
| public static FuncotationMap createAsAllTableFuncotationsFromVcf(final String transcriptFieldName, final String[] funcotationKeys, | ||
| final String funcotationAttributeForSingleAllele, final Allele altAllele, | ||
| final String datasourceName) { | ||
| Utils.nonNull(transcriptFieldName); | ||
| Utils.nonNull(funcotationKeys); | ||
| Utils.nonNull(funcotationAttributeForSingleAllele); | ||
| Utils.nonNull(altAllele); | ||
| Utils.nonNull(datasourceName); | ||
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| final FuncotationMap result = createEmpty(); | ||
| final String[] funcotationAttributeForSingleAlleleByTranscript = StringUtils.splitByWholeSeparator(funcotationAttributeForSingleAllele, "]#["); | ||
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| for (final String funcotationAttribute : funcotationAttributeForSingleAlleleByTranscript) { | ||
| final String[] values = StringUtils.splitByWholeSeparatorPreserveAllTokens(funcotationAttribute, "|"); | ||
| if (values[0].startsWith(VcfOutputRenderer.START_TRANSCRIPT_DELIMITER)) { | ||
| values[0] = values[0].replace(VcfOutputRenderer.START_TRANSCRIPT_DELIMITER, ""); | ||
| } | ||
| if (values[values.length - 1].endsWith(VcfOutputRenderer.END_TRANSCRIPT_DELIMITER)) { | ||
| values[values.length - 1] = values[values.length - 1].replace(VcfOutputRenderer.END_TRANSCRIPT_DELIMITER, ""); | ||
| } | ||
| if (values.length != funcotationKeys.length) { | ||
| logger.error("Keys: " + StringUtils.join(funcotationKeys, ", ")); | ||
| logger.error("Values: " + StringUtils.join(values, ", ")); | ||
| throw new GATKException.ShouldNeverReachHereException("Cannot parse the funcotation attribute. Num values: " + values.length + " Num keys: " + funcotationKeys.length); | ||
| } | ||
| final Map<String, String> simpleNameValuePairs = IntStream.range(0, values.length).boxed().collect(Collectors | ||
| .toMap(i -> funcotationKeys[i], i-> values[i])); | ||
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| final List<String> valuesAsList = Arrays.asList(funcotationKeys).stream().map(k -> simpleNameValuePairs.get(k)).collect(Collectors.toList()); | ||
| result.add(simpleNameValuePairs.getOrDefault(transcriptFieldName, NO_TRANSCRIPT_AVAILABLE_KEY), new TableFuncotation(Arrays.asList(funcotationKeys), valuesAsList, altAllele, datasourceName)); | ||
|
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| } | ||
| return result; | ||
| } | ||
|
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| private static boolean areDuplicateTranscriptIDsFound(final List<GencodeFuncotation> gencodeFuncotations) { | ||
| return gencodeFuncotations.size() != new HashSet<>(gencodeFuncotations).size(); | ||
| } | ||
| } |
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