badData;
+
/**
- * Constructor given an alignment context
+ * Constructor given a VCF file
*
* @param alignment
*/
- public VCFLoader(AlignmentI alignment)
+ public VCFLoader(String vcfFile)
{
- al = alignment;
+ try
+ {
+ initialise(vcfFile);
+ } catch (IOException e)
+ {
+ System.err.println("Error opening VCF file: " + e.getMessage());
+ }
// map of species!chromosome!fromAssembly!toAssembly to {fromRange, toRange}
assemblyMappings = new HashMap<>();
}
/**
- * Starts a new thread to query and load VCF variant data on to the alignment
+ * Starts a new thread to query and load VCF variant data on to the given
+ * sequences
*
* This method is not thread safe - concurrent threads should use separate
* instances of this class.
*
- * @param filePath
+ * @param seqs
* @param gui
*/
- public void loadVCF(final String filePath,
- final AlignViewControllerGuiI gui)
+ public void loadVCF(SequenceI[] seqs, final AlignViewControllerGuiI gui)
{
if (gui != null)
{
@@ -181,46 +293,70 @@ public class VCFLoader
new Thread()
{
-
@Override
public void run()
{
- VCFLoader.this.doLoad(filePath, gui);
+ VCFLoader.this.doLoad(seqs, gui);
}
-
}.start();
}
/**
- * Loads VCF on to an alignment - provided it can be related to one or more
- * sequence's chromosomal coordinates
+ * Reads the specified contig sequence and adds its VCF variants to it
*
- * @param filePath
- * @param gui
- * optional callback handler for messages
+ * @param contig
+ * the id of a single sequence (contig) to load
+ * @return
*/
- protected void doLoad(String filePath, AlignViewControllerGuiI gui)
+ public SequenceI loadVCFContig(String contig)
{
- VCFReader reader = null;
- try
+ VCFHeaderLine headerLine = header.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
+ if (headerLine == null)
{
- // long start = System.currentTimeMillis();
- reader = new VCFReader(filePath);
-
- header = reader.getFileHeader();
+ Cache.log.error("VCF reference header not found");
+ return null;
+ }
+ String ref = headerLine.getValue();
+ if (ref.startsWith("file://"))
+ {
+ ref = ref.substring(7);
+ }
+ setSpeciesAndAssembly(ref);
- sourceId = filePath;
+ SequenceI seq = null;
+ File dbFile = new File(ref);
- saveMetadata(sourceId);
+ if (dbFile.exists())
+ {
+ HtsContigDb db = new HtsContigDb("", dbFile);
+ seq = db.getSequenceProxy(contig);
+ loadSequenceVCF(seq);
+ db.close();
+ }
+ else
+ {
+ Cache.log.error("VCF reference not found: " + ref);
+ }
- /*
- * get offset of CSQ ALLELE_NUM and Feature if declared
- */
- parseCsqHeader();
+ return seq;
+ }
+ /**
+ * Loads VCF on to one or more sequences
+ *
+ * @param seqs
+ * @param gui
+ * optional callback handler for messages
+ */
+ protected void doLoad(SequenceI[] seqs, AlignViewControllerGuiI gui)
+ {
+ try
+ {
VCFHeaderLine ref = header
.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
- String vcfAssembly = ref.getValue();
+ String reference = ref == null ? null : ref.getValue();
+
+ setSpeciesAndAssembly(reference);
int varCount = 0;
int seqCount = 0;
@@ -228,9 +364,9 @@ public class VCFLoader
/*
* query for VCF overlapping each sequence in turn
*/
- for (SequenceI seq : al.getSequences())
+ for (SequenceI seq : seqs)
{
- int added = loadSequenceVCF(seq, reader, vcfAssembly);
+ int added = loadSequenceVCF(seq);
if (added > 0)
{
seqCount++;
@@ -240,7 +376,6 @@ public class VCFLoader
}
if (gui != null)
{
- // long elapsed = System.currentTimeMillis() - start;
String msg = MessageManager.formatMessage("label.added_vcf",
varCount, seqCount);
gui.setStatus(msg);
@@ -269,7 +404,106 @@ public class VCFLoader
// ignore
}
}
+ header = null;
+ dictionary = null;
+ }
+ }
+
+ /**
+ * Attempts to determine and save the species and genome assembly version to
+ * which the VCF data applies. This may be done by parsing the {@code reference}
+ * header line, configured in a property file, or (potentially) confirmed
+ * interactively by the user.
+ *
+ * The saved values should be identifiers valid for Ensembl's REST service
+ * {@code map} endpoint, so they can be used (if necessary) to retrieve the
+ * mapping between VCF coordinates and sequence coordinates.
+ *
+ * @param reference
+ * @see https://rest.ensembl.org/documentation/info/assembly_map
+ * @see https://rest.ensembl.org/info/assembly/human?content-type=text/xml
+ * @see https://rest.ensembl.org/info/species?content-type=text/xml
+ */
+ protected void setSpeciesAndAssembly(String reference)
+ {
+ if (reference == null)
+ {
+ Cache.log.error("No VCF ##reference found, defaulting to "
+ + DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
+ reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
+ }
+ reference = reference.toLowerCase();
+
+ /*
+ * for a non-human species, or other assembly identifier,
+ * specify as a Jalview property file entry e.g.
+ * VCF_ASSEMBLY = hs37=GRCh37,assembly19=GRCh37
+ * VCF_SPECIES = c_elegans=celegans
+ * to map a token in the reference header to a value
+ */
+ String prop = Cache.getDefault(VCF_ASSEMBLY, DEFAULT_VCF_ASSEMBLY);
+ for (String token : prop.split(","))
+ {
+ String[] tokens = token.split("=");
+ if (tokens.length == 2)
+ {
+ if (reference.contains(tokens[0].trim().toLowerCase()))
+ {
+ vcfAssembly = tokens[1].trim();
+ break;
+ }
+ }
+ }
+
+ vcfSpecies = DEFAULT_SPECIES;
+ prop = Cache.getProperty(VCF_SPECIES);
+ if (prop != null)
+ {
+ for (String token : prop.split(","))
+ {
+ String[] tokens = token.split("=");
+ if (tokens.length == 2)
+ {
+ if (reference.contains(tokens[0].trim().toLowerCase()))
+ {
+ vcfSpecies = tokens[1].trim();
+ break;
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Opens the VCF file and parses header data
+ *
+ * @param filePath
+ * @throws IOException
+ */
+ private void initialise(String filePath) throws IOException
+ {
+ vcfFilePath = filePath;
+
+ reader = new VCFReader(filePath);
+
+ header = reader.getFileHeader();
+
+ try
+ {
+ dictionary = header.getSequenceDictionary();
+ } catch (SAMException e)
+ {
+ // ignore - thrown if any contig line lacks length info
}
+
+ sourceId = filePath;
+
+ saveMetadata(sourceId);
+
+ /*
+ * get offset of CSQ ALLELE_NUM and Feature if declared
+ */
+ parseCsqHeader();
}
/**
@@ -378,15 +612,19 @@ public class VCFLoader
int index = 0;
for (String field : format)
{
- if (ALLELE_NUM_KEY.equals(field))
+ if (CSQ_CONSEQUENCE_KEY.equals(field))
+ {
+ csqConsequenceFieldIndex = index;
+ }
+ if (CSQ_ALLELE_NUM_KEY.equals(field))
{
csqAlleleNumberFieldIndex = index;
}
- if (ALLELE_KEY.equals(field))
+ if (CSQ_ALLELE_KEY.equals(field))
{
csqAlleleFieldIndex = index;
}
- if (FEATURE_KEY.equals(field))
+ if (CSQ_FEATURE_KEY.equals(field))
{
csqFeatureFieldIndex = index;
}
@@ -462,7 +700,8 @@ public class VCFLoader
/*
* dna-to-peptide product mapping
*/
- AlignmentUtils.computeProteinFeatures(seq, mapTo, map);
+ // JAL-3187 render on the fly instead
+ // AlignmentUtils.computeProteinFeatures(seq, mapTo, map);
}
else
{
@@ -483,194 +722,202 @@ public class VCFLoader
}
/**
- * Tries to add overlapping variants read from a VCF file to the given
- * sequence, and returns the number of variant features added. Note that this
- * requires the sequence to hold information as to its species, chromosomal
- * positions and reference assembly, in order to be able to map the VCF
- * variants to the sequence (or not)
+ * Tries to add overlapping variants read from a VCF file to the given sequence,
+ * and returns the number of variant features added
*
* @param seq
- * @param reader
- * @param vcfAssembly
* @return
*/
- protected int loadSequenceVCF(SequenceI seq, VCFReader reader,
- String vcfAssembly)
+ protected int loadSequenceVCF(SequenceI seq)
{
- int count = 0;
- GeneLociI seqCoords = seq.getGeneLoci();
- if (seqCoords == null)
+ VCFMap vcfMap = getVcfMap(seq);
+ if (vcfMap == null)
{
- System.out.println(String.format(
- "Can't query VCF for %s as chromosome coordinates not known",
- seq.getName()));
return 0;
}
- if (!vcfSpeciesMatchesSequence(vcfAssembly, seqCoords.getSpeciesId()))
- {
- return 0;
- }
-
- List seqChromosomalContigs = seqCoords.getMap().getToRanges();
- for (int[] range : seqChromosomalContigs)
+ /*
+ * work with the dataset sequence here
+ */
+ SequenceI dss = seq.getDatasetSequence();
+ if (dss == null)
{
- count += addVcfVariants(seq, reader, range, vcfAssembly);
+ dss = seq;
}
-
- return count;
+ return addVcfVariants(dss, vcfMap);
}
/**
- * Answers true if the species inferred from the VCF reference identifier
- * matches that for the sequence
+ * Answers a map from sequence coordinates to VCF chromosome ranges
*
- * @param vcfAssembly
- * @param speciesId
+ * @param seq
* @return
*/
- boolean vcfSpeciesMatchesSequence(String vcfAssembly, String speciesId)
+ private VCFMap getVcfMap(SequenceI seq)
{
- // PROBLEM 1
- // there are many aliases for species - how to equate one with another?
- // PROBLEM 2
- // VCF ##reference header is an unstructured URI - how to extract species?
- // perhaps check if ref includes any (Ensembl) alias of speciesId??
- // TODO ask the user to confirm this??
-
- if (vcfAssembly.contains("Homo_sapiens") // gnomAD exome data example
- && "HOMO_SAPIENS".equals(speciesId)) // Ensembl species id
+ /*
+ * simplest case: sequence has id and length matching a VCF contig
+ */
+ VCFMap vcfMap = null;
+ if (dictionary != null)
{
- return true;
+ vcfMap = getContigMap(seq);
}
-
- if (vcfAssembly.contains("c_elegans") // VEP VCF response example
- && "CAENORHABDITIS_ELEGANS".equals(speciesId)) // Ensembl
+ if (vcfMap != null)
{
- return true;
+ return vcfMap;
}
- // this is not a sustainable solution...
-
- return false;
- }
-
- /**
- * Queries the VCF reader for any variants that overlap the given chromosome
- * region of the sequence, and adds as variant features. Returns the number of
- * overlapping variants found.
- *
- * @param seq
- * @param reader
- * @param range
- * start-end range of a sequence region in its chromosomal
- * coordinates
- * @param vcfAssembly
- * the '##reference' identifier for the VCF reference assembly
- * @return
- */
- protected int addVcfVariants(SequenceI seq, VCFReader reader,
- int[] range, String vcfAssembly)
- {
+ /*
+ * otherwise, map to VCF from chromosomal coordinates
+ * of the sequence (if known)
+ */
GeneLociI seqCoords = seq.getGeneLoci();
+ if (seqCoords == null)
+ {
+ Cache.log.warn(String.format(
+ "Can't query VCF for %s as chromosome coordinates not known",
+ seq.getName()));
+ return null;
+ }
+ String species = seqCoords.getSpeciesId();
String chromosome = seqCoords.getChromosomeId();
String seqRef = seqCoords.getAssemblyId();
- String species = seqCoords.getSpeciesId();
+ MapList map = seqCoords.getMapping();
- /*
- * map chromosomal coordinates from sequence to VCF if the VCF
- * data has a different reference assembly to the sequence
- */
- // TODO generalise for non-human species
- // - or get the user to choose in a dialog
-
- int offset = 0;
- if ("GRCh38".equalsIgnoreCase(seqRef) // Ensembl
- && vcfAssembly.contains("Homo_sapiens_assembly19")) // gnomAD
+ // note this requires the configured species to match that
+ // returned with the Ensembl sequence; todo: support aliases?
+ if (!vcfSpecies.equalsIgnoreCase(species))
{
- String toRef = "GRCh37";
- int[] newRange = mapReferenceRange(range, chromosome, "human",
- seqRef, toRef);
- if (newRange == null)
- {
- System.err.println(String.format(
- "Failed to map %s:%s:%s:%d:%d to %s", species, chromosome,
- seqRef, range[0], range[1], toRef));
- return 0;
- }
- offset = newRange[0] - range[0];
- range = newRange;
+ Cache.log.warn("No VCF loaded to " + seq.getName()
+ + " as species not matched");
+ return null;
}
- boolean forwardStrand = range[0] <= range[1];
+ if (seqRef.equalsIgnoreCase(vcfAssembly))
+ {
+ return new VCFMap(chromosome, map);
+ }
/*
- * query the VCF for overlaps
- * (convert a reverse strand range to forwards)
+ * VCF data has a different reference assembly to the sequence:
+ * query Ensembl to map chromosomal coordinates from sequence to VCF
*/
- int count = 0;
- MapList mapping = seqCoords.getMap();
+ List toVcfRanges = new ArrayList<>();
+ List fromSequenceRanges = new ArrayList<>();
- int fromLocus = Math.min(range[0], range[1]);
- int toLocus = Math.max(range[0], range[1]);
- CloseableIterator variants = reader.query(chromosome,
- fromLocus, toLocus);
- while (variants.hasNext())
+ for (int[] range : map.getToRanges())
{
- /*
- * get variant location in sequence chromosomal coordinates
- */
- VariantContext variant = variants.next();
-
- int start = variant.getStart() - offset;
- int end = variant.getEnd() - offset;
+ int[] fromRange = map.locateInFrom(range[0], range[1]);
+ if (fromRange == null)
+ {
+ // corrupted map?!?
+ continue;
+ }
- /*
- * convert chromosomal location to sequence coordinates
- * - may be reverse strand (convert to forward for sequence feature)
- * - null if a partially overlapping feature
- */
- int[] seqLocation = mapping.locateInFrom(start, end);
- if (seqLocation != null)
+ int[] newRange = mapReferenceRange(range, chromosome, "human", seqRef,
+ vcfAssembly);
+ if (newRange == null)
{
- int featureStart = Math.min(seqLocation[0], seqLocation[1]);
- int featureEnd = Math.max(seqLocation[0], seqLocation[1]);
- count += addAlleleFeatures(seq, variant, featureStart, featureEnd,
- forwardStrand);
+ Cache.log.error(
+ String.format("Failed to map %s:%s:%s:%d:%d to %s", species,
+ chromosome, seqRef, range[0], range[1],
+ vcfAssembly));
+ continue;
+ }
+ else
+ {
+ toVcfRanges.add(newRange);
+ fromSequenceRanges.add(fromRange);
}
}
- variants.close();
+ return new VCFMap(chromosome,
+ new MapList(fromSequenceRanges, toVcfRanges, 1, 1));
+ }
- return count;
+ /**
+ * If the sequence id matches a contig declared in the VCF file, and the
+ * sequence length matches the contig length, then returns a 1:1 map of the
+ * sequence to the contig, else returns null
+ *
+ * @param seq
+ * @return
+ */
+ private VCFMap getContigMap(SequenceI seq)
+ {
+ String id = seq.getName();
+ SAMSequenceRecord contig = dictionary.getSequence(id);
+ if (contig != null)
+ {
+ int len = seq.getLength();
+ if (len == contig.getSequenceLength())
+ {
+ MapList map = new MapList(new int[] { 1, len },
+ new int[]
+ { 1, len }, 1, 1);
+ return new VCFMap(id, map);
+ }
+ }
+ return null;
}
/**
- * A convenience method to get the AF value for the given alternate allele
- * index
+ * Queries the VCF reader for any variants that overlap the mapped chromosome
+ * ranges of the sequence, and adds as variant features. Returns the number of
+ * overlapping variants found.
*
- * @param variant
- * @param alleleIndex
+ * @param seq
+ * @param map
+ * mapping from sequence to VCF coordinates
* @return
*/
- protected float getAlleleFrequency(VariantContext variant, int alleleIndex)
+ protected int addVcfVariants(SequenceI seq, VCFMap map)
{
- float score = 0f;
- String attributeValue = getAttributeValue(variant,
- ALLELE_FREQUENCY_KEY, alleleIndex);
- if (attributeValue != null)
+ boolean forwardStrand = map.map.isToForwardStrand();
+
+ /*
+ * query the VCF for overlaps of each contiguous chromosomal region
+ */
+ int count = 0;
+
+ for (int[] range : map.map.getToRanges())
{
+ int vcfStart = Math.min(range[0], range[1]);
+ int vcfEnd = Math.max(range[0], range[1]);
try
{
- score = Float.parseFloat(attributeValue);
- } catch (NumberFormatException e)
+ CloseableIterator variants = reader
+ .query(map.chromosome, vcfStart, vcfEnd);
+ while (variants.hasNext())
+ {
+ VariantContext variant = variants.next();
+
+ int[] featureRange = map.map.locateInFrom(variant.getStart(),
+ variant.getEnd());
+
+ if (featureRange != null)
+ {
+ int featureStart = Math.min(featureRange[0], featureRange[1]);
+ int featureEnd = Math.max(featureRange[0], featureRange[1]);
+ count += addAlleleFeatures(seq, variant, featureStart,
+ featureEnd, forwardStrand);
+ }
+ }
+ variants.close();
+ } catch (TribbleException e)
{
- // leave as 0
+ /*
+ * RuntimeException throwable by htsjdk
+ */
+ String msg = String.format("Error reading VCF for %s:%d-%d: %s ",
+ map.chromosome, vcfStart, vcfEnd,e.getLocalizedMessage());
+ Cache.log.error(msg);
}
}
- return score;
+ return count;
}
/**
@@ -729,9 +976,9 @@ public class VCFLoader
/**
* Inspects one allele and attempts to add a variant feature for it to the
- * sequence. We extract as much as possible of the additional data associated
- * with this allele to store in the feature's key-value map. Answers the
- * number of features added (0 or 1).
+ * sequence. The additional data associated with this allele is extracted to
+ * store in the feature's key-value map. Answers the number of features added (0
+ * or 1).
*
* @param seq
* @param variant
@@ -751,26 +998,68 @@ public class VCFLoader
String allele = alt.getBaseString();
/*
+ * insertion after a genomic base, if on reverse strand, has to be
+ * converted to insertion of complement after the preceding position
+ */
+ int referenceLength = reference.length();
+ if (!forwardStrand && allele.length() > referenceLength
+ && allele.startsWith(reference))
+ {
+ featureStart -= referenceLength;
+ featureEnd = featureStart;
+ char insertAfter = seq.getCharAt(featureStart - seq.getStart());
+ reference = Dna.reverseComplement(String.valueOf(insertAfter));
+ allele = allele.substring(referenceLength) + reference;
+ }
+
+ /*
* build the ref,alt allele description e.g. "G,A", using the base
* complement if the sequence is on the reverse strand
*/
- // TODO check how structural variants are shown on reverse strand
StringBuilder sb = new StringBuilder();
sb.append(forwardStrand ? reference : Dna.reverseComplement(reference));
sb.append(COMMA);
sb.append(forwardStrand ? allele : Dna.reverseComplement(allele));
String alleles = sb.toString(); // e.g. G,A
+ /*
+ * pick out the consequence data (if any) that is for the current allele
+ * and feature (transcript) that matches the current sequence
+ */
+ String consequence = getConsequenceForAlleleAndFeature(variant, CSQ_FIELD,
+ altAlleleIndex, csqAlleleFieldIndex,
+ csqAlleleNumberFieldIndex, seq.getName().toLowerCase(),
+ csqFeatureFieldIndex);
+
+ /*
+ * pick out the ontology term for the consequence type
+ */
String type = SequenceOntologyI.SEQUENCE_VARIANT;
- float score = getAlleleFrequency(variant, altAlleleIndex);
+ if (consequence != null)
+ {
+ type = getOntologyTerm(consequence);
+ }
SequenceFeature sf = new SequenceFeature(type, alleles, featureStart,
- featureEnd, score, FEATURE_GROUP_VCF);
+ featureEnd, FEATURE_GROUP_VCF);
sf.setSource(sourceId);
- sf.setValue(Gff3Helper.ALLELES, alleles);
+ /*
+ * save the derived alleles as a named attribute; this will be
+ * needed when Jalview computes derived peptide variants
+ */
+ addFeatureAttribute(sf, Gff3Helper.ALLELES, alleles);
- addAlleleProperties(variant, seq, sf, altAlleleIndex);
+ /*
+ * add selected VCF fixed column data as feature attributes
+ */
+ addFeatureAttribute(sf, VCF_POS, String.valueOf(variant.getStart()));
+ addFeatureAttribute(sf, VCF_ID, variant.getID());
+ addFeatureAttribute(sf, VCF_QUAL,
+ String.valueOf(variant.getPhredScaledQual()));
+ addFeatureAttribute(sf, VCF_FILTER, getFilter(variant));
+
+ addAlleleProperties(variant, sf, altAlleleIndex, consequence);
seq.addSequenceFeature(sf);
@@ -778,16 +1067,220 @@ public class VCFLoader
}
/**
+ * Answers the VCF FILTER value for the variant - or an approximation to it.
+ * This field is either PASS, or a semi-colon separated list of filters not
+ * passed. htsjdk saves filters as a HashSet, so the order when reassembled into
+ * a list may be different.
+ *
+ * @param variant
+ * @return
+ */
+ String getFilter(VariantContext variant)
+ {
+ Set filters = variant.getFilters();
+ if (filters.isEmpty())
+ {
+ return NO_VALUE;
+ }
+ Iterator iterator = filters.iterator();
+ String first = iterator.next();
+ if (filters.size() == 1)
+ {
+ return first;
+ }
+
+ StringBuilder sb = new StringBuilder(first);
+ while (iterator.hasNext())
+ {
+ sb.append(";").append(iterator.next());
+ }
+
+ return sb.toString();
+ }
+
+ /**
+ * Adds one feature attribute unless the value is null, empty or '.'
+ *
+ * @param sf
+ * @param key
+ * @param value
+ */
+ void addFeatureAttribute(SequenceFeature sf, String key, String value)
+ {
+ if (value != null && !value.isEmpty() && !NO_VALUE.equals(value))
+ {
+ sf.setValue(key, value);
+ }
+ }
+
+ /**
+ * Determines the Sequence Ontology term to use for the variant feature type in
+ * Jalview. The default is 'sequence_variant', but a more specific term is used
+ * if:
+ *
+ * - VEP (or SnpEff) Consequence annotation is included in the VCF
+ * - sequence id can be matched to VEP Feature (or SnpEff Feature_ID)
+ *
+ *
+ * @param consequence
+ * @return
+ * @see http://www.sequenceontology.org/browser/current_svn/term/SO:0001060
+ */
+ String getOntologyTerm(String consequence)
+ {
+ String type = SequenceOntologyI.SEQUENCE_VARIANT;
+
+ /*
+ * could we associate Consequence data with this allele and feature (transcript)?
+ * if so, prefer the consequence term from that data
+ */
+ if (csqAlleleFieldIndex == -1) // && snpEffAlleleFieldIndex == -1
+ {
+ /*
+ * no Consequence data so we can't refine the ontology term
+ */
+ return type;
+ }
+
+ if (consequence != null)
+ {
+ String[] csqFields = consequence.split(PIPE_REGEX);
+ if (csqFields.length > csqConsequenceFieldIndex)
+ {
+ type = csqFields[csqConsequenceFieldIndex];
+ }
+ }
+ else
+ {
+ // todo the same for SnpEff consequence data matching if wanted
+ }
+
+ /*
+ * if of the form (e.g.) missense_variant&splice_region_variant,
+ * just take the first ('most severe') consequence
+ */
+ if (type != null)
+ {
+ int pos = type.indexOf('&');
+ if (pos > 0)
+ {
+ type = type.substring(0, pos);
+ }
+ }
+ return type;
+ }
+
+ /**
+ * Returns matched consequence data if it can be found, else null.
+ *
+ * - inspects the VCF data for key 'vcfInfoId'
+ * - splits this on comma (to distinct consequences)
+ * - returns the first consequence (if any) where
+ *
+ * - the allele matches the altAlleleIndex'th allele of variant
+ * - the feature matches the sequence name (e.g. transcript id)
+ *
+ *
+ * If matched, the consequence is returned (as pipe-delimited fields).
+ *
+ * @param variant
+ * @param vcfInfoId
+ * @param altAlleleIndex
+ * @param alleleFieldIndex
+ * @param alleleNumberFieldIndex
+ * @param seqName
+ * @param featureFieldIndex
+ * @return
+ */
+ private String getConsequenceForAlleleAndFeature(VariantContext variant,
+ String vcfInfoId, int altAlleleIndex, int alleleFieldIndex,
+ int alleleNumberFieldIndex,
+ String seqName, int featureFieldIndex)
+ {
+ if (alleleFieldIndex == -1 || featureFieldIndex == -1)
+ {
+ return null;
+ }
+ Object value = variant.getAttribute(vcfInfoId);
+
+ if (value == null || !(value instanceof List))
+ {
+ return null;
+ }
+
+ /*
+ * inspect each consequence in turn (comma-separated blocks
+ * extracted by htsjdk)
+ */
+ List consequences = (List) value;
+
+ for (String consequence : consequences)
+ {
+ String[] csqFields = consequence.split(PIPE_REGEX);
+ if (csqFields.length > featureFieldIndex)
+ {
+ String featureIdentifier = csqFields[featureFieldIndex];
+ if (featureIdentifier.length() > 4
+ && seqName.indexOf(featureIdentifier.toLowerCase()) > -1)
+ {
+ /*
+ * feature (transcript) matched - now check for allele match
+ */
+ if (matchAllele(variant, altAlleleIndex, csqFields,
+ alleleFieldIndex, alleleNumberFieldIndex))
+ {
+ return consequence;
+ }
+ }
+ }
+ }
+ return null;
+ }
+
+ private boolean matchAllele(VariantContext variant, int altAlleleIndex,
+ String[] csqFields, int alleleFieldIndex,
+ int alleleNumberFieldIndex)
+ {
+ /*
+ * if ALLELE_NUM is present, it must match altAlleleIndex
+ * NB first alternate allele is 1 for ALLELE_NUM, 0 for altAlleleIndex
+ */
+ if (alleleNumberFieldIndex > -1)
+ {
+ if (csqFields.length <= alleleNumberFieldIndex)
+ {
+ return false;
+ }
+ String alleleNum = csqFields[alleleNumberFieldIndex];
+ return String.valueOf(altAlleleIndex + 1).equals(alleleNum);
+ }
+
+ /*
+ * else consequence allele must match variant allele
+ */
+ if (alleleFieldIndex > -1 && csqFields.length > alleleFieldIndex)
+ {
+ String csqAllele = csqFields[alleleFieldIndex];
+ String vcfAllele = variant.getAlternateAllele(altAlleleIndex)
+ .getBaseString();
+ return csqAllele.equals(vcfAllele);
+ }
+ return false;
+ }
+
+ /**
* Add any allele-specific VCF key-value data to the sequence feature
*
* @param variant
- * @param seq
* @param sf
* @param altAlelleIndex
* (0, 1..)
+ * @param consequence
+ * if not null, the consequence specific to this sequence (transcript
+ * feature) and allele
*/
- protected void addAlleleProperties(VariantContext variant, SequenceI seq,
- SequenceFeature sf, final int altAlelleIndex)
+ protected void addAlleleProperties(VariantContext variant,
+ SequenceFeature sf, final int altAlelleIndex, String consequence)
{
Map atts = variant.getAttributes();
@@ -801,7 +1294,7 @@ public class VCFLoader
*/
if (CSQ_FIELD.equals(key))
{
- addConsequences(variant, seq, sf, altAlelleIndex);
+ addConsequences(variant, sf, consequence);
continue;
}
@@ -850,39 +1343,102 @@ public class VCFLoader
* take the index'th value
*/
String value = getAttributeValue(variant, key, index);
- if (value != null)
+ if (value != null && isValid(variant, key, value))
+ {
+ /*
+ * decode colon, semicolon, equals sign, percent sign, comma (only)
+ * as required by the VCF specification (para 1.2)
+ */
+ value = StringUtils.urlDecode(value, VCF_ENCODABLE);
+ addFeatureAttribute(sf, key, value);
+ }
+ }
+ }
+
+ /**
+ * Answers true for '.', null, or an empty value, or if the INFO type is String.
+ * If the INFO type is Integer or Float, answers false if the value is not in
+ * valid format.
+ *
+ * @param variant
+ * @param infoId
+ * @param value
+ * @return
+ */
+ protected boolean isValid(VariantContext variant, String infoId,
+ String value)
+ {
+ if (value == null || value.isEmpty() || NO_VALUE.equals(value))
+ {
+ return true;
+ }
+ VCFInfoHeaderLine infoHeader = header.getInfoHeaderLine(infoId);
+ if (infoHeader == null)
+ {
+ Cache.log.error("Field " + infoId + " has no INFO header");
+ return false;
+ }
+ VCFHeaderLineType infoType = infoHeader.getType();
+ try
+ {
+ if (infoType == VCFHeaderLineType.Integer)
+ {
+ Integer.parseInt(value);
+ }
+ else if (infoType == VCFHeaderLineType.Float)
{
- sf.setValue(key, value);
+ Float.parseFloat(value);
}
+ } catch (NumberFormatException e)
+ {
+ logInvalidValue(variant, infoId, value);
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Logs an error message for malformed data; duplicate messages (same id and
+ * value) are not logged
+ *
+ * @param variant
+ * @param infoId
+ * @param value
+ */
+ private void logInvalidValue(VariantContext variant, String infoId,
+ String value)
+ {
+ if (badData == null)
+ {
+ badData = new HashSet<>();
+ }
+ String token = infoId + ":" + value;
+ if (!badData.contains(token))
+ {
+ badData.add(token);
+ Cache.log.error(String.format("Invalid VCF data at %s:%d %s=%s",
+ variant.getContig(), variant.getStart(), infoId, value));
}
}
/**
* Inspects CSQ data blocks (consequences) and adds attributes on the sequence
- * feature for the current allele (and transcript if applicable)
+ * feature.
*
- * Allele matching: if field ALLELE_NUM is present, it must match
- * altAlleleIndex. If not present, then field Allele value must match the VCF
- * Allele.
- *
- * Transcript matching: if sequence name can be identified to at least one of
- * the consequences' Feature values, then select only consequences that match
- * the value (i.e. consequences for the current transcript sequence). If not,
- * take all consequences (this is the case when adding features to the gene
- * sequence).
+ * If myConsequence is not null, then this is the specific
+ * consequence data (pipe-delimited fields) that is for the current allele and
+ * transcript (sequence) being processed)
*
* @param variant
- * @param seq
* @param sf
- * @param altAlelleIndex
- * (0, 1..)
+ * @param myConsequence
*/
- protected void addConsequences(VariantContext variant, SequenceI seq,
- SequenceFeature sf, int altAlelleIndex)
+ protected void addConsequences(VariantContext variant, SequenceFeature sf,
+ String myConsequence)
{
Object value = variant.getAttribute(CSQ_FIELD);
- if (value == null || !(value instanceof ArrayList))
+ if (value == null || !(value instanceof List))
{
return;
}
@@ -890,43 +1446,17 @@ public class VCFLoader
List consequences = (List) value;
/*
- * if CSQ data includes 'Feature', and any value matches the sequence name,
- * then restrict consequence data to only the matching value (transcript)
- * i.e. just pick out consequences for the transcript the variant feature is on
- */
- String seqName = seq.getName()== null ? "" : seq.getName().toLowerCase();
- String matchFeature = null;
- if (csqFeatureFieldIndex > -1)
- {
- for (String consequence : consequences)
- {
- String[] csqFields = consequence.split(PIPE_REGEX);
- if (csqFields.length > csqFeatureFieldIndex)
- {
- String featureIdentifier = csqFields[csqFeatureFieldIndex];
- if (featureIdentifier.length() > 4
- && seqName.indexOf(featureIdentifier.toLowerCase()) > -1)
- {
- matchFeature = featureIdentifier;
- }
- }
- }
- }
-
- /*
- * inspect CSQ consequences; where possible restrict to the consequence
+ * inspect CSQ consequences; restrict to the consequence
* associated with the current transcript (Feature)
*/
- SortedMap csqValues = new TreeMap<>(
- String.CASE_INSENSITIVE_ORDER);
+ Map csqValues = new HashMap<>();
for (String consequence : consequences)
{
- String[] csqFields = consequence.split(PIPE_REGEX);
-
- if (includeConsequence(csqFields, matchFeature, variant,
- altAlelleIndex))
+ if (myConsequence == null || myConsequence.equals(consequence))
{
+ String[] csqFields = consequence.split(PIPE_REGEX);
+
/*
* inspect individual fields of this consequence, copying non-null
* values which are 'fields of interest'
@@ -939,6 +1469,11 @@ public class VCFLoader
String id = vepFieldsOfInterest.get(i);
if (id != null)
{
+ /*
+ * VCF spec requires encoding of special characters e.g. '='
+ * so decode them here before storing
+ */
+ field = StringUtils.urlDecode(field, VCF_ENCODABLE);
csqValues.put(id, field);
}
}
@@ -954,72 +1489,6 @@ public class VCFLoader
}
/**
- * Answers true if we want to associate this block of consequence data with
- * the specified alternate allele of the VCF variant.
- *
- * If consequence data includes the ALLELE_NUM field, then this has to match
- * altAlleleIndex. Otherwise the Allele field of the consequence data has to
- * match the allele value.
- *
- * Optionally (if matchFeature is not null), restrict to only include
- * consequences whose Feature value matches. This allows us to attach
- * consequences to their respective transcripts.
- *
- * @param csqFields
- * @param matchFeature
- * @param variant
- * @param altAlelleIndex
- * (0, 1..)
- * @return
- */
- protected boolean includeConsequence(String[] csqFields,
- String matchFeature, VariantContext variant, int altAlelleIndex)
- {
- /*
- * check consequence is for the current transcript
- */
- if (matchFeature != null)
- {
- if (csqFields.length <= csqFeatureFieldIndex)
- {
- return false;
- }
- String featureIdentifier = csqFields[csqFeatureFieldIndex];
- if (!featureIdentifier.equals(matchFeature))
- {
- return false; // consequence is for a different transcript
- }
- }
-
- /*
- * if ALLELE_NUM is present, it must match altAlleleIndex
- * NB first alternate allele is 1 for ALLELE_NUM, 0 for altAlleleIndex
- */
- if (csqAlleleNumberFieldIndex > -1)
- {
- if (csqFields.length <= csqAlleleNumberFieldIndex)
- {
- return false;
- }
- String alleleNum = csqFields[csqAlleleNumberFieldIndex];
- return String.valueOf(altAlelleIndex + 1).equals(alleleNum);
- }
-
- /*
- * else consequence allele must match variant allele
- */
- if (csqAlleleFieldIndex > -1 && csqFields.length > csqAlleleFieldIndex)
- {
- String csqAllele = csqFields[csqAlleleFieldIndex];
- String vcfAllele = variant.getAlternateAllele(altAlelleIndex)
- .getBaseString();
- return csqAllele.equals(vcfAllele);
- }
-
- return false;
- }
-
- /**
* A convenience method to complement a dna base and return the string value
* of its complement
*