>();
+ assemblyMappings = new HashMap<>();
}
/**
- * Loads VCF on to an alignment - provided it can be related to one or more
- * sequence's chromosomal coordinates.
+ * 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 status
+ * @param seqs
+ * @param gui
*/
- public void loadVCF(String filePath, AlignViewControllerGuiI status)
+ public void loadVCF(SequenceI[] seqs, final AlignViewControllerGuiI gui)
{
- VCFReader reader = null;
+ if (gui != null)
+ {
+ gui.setStatus(MessageManager.getString("label.searching_vcf"));
+ }
- try
+ new Thread()
+ {
+ @Override
+ public void run()
+ {
+ VCFLoader.this.doLoad(seqs, gui);
+ }
+ }.start();
+ }
+
+ /**
+ * Reads the specified contig sequence and adds its VCF variants to it
+ *
+ * @param contig
+ * the id of a single sequence (contig) to load
+ * @return
+ */
+ public SequenceI loadVCFContig(String contig)
+ {
+ VCFHeaderLine headerLine = header.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
+ if (headerLine == null)
+ {
+ Cache.error("VCF reference header not found");
+ return null;
+ }
+ String ref = headerLine.getValue();
+ if (ref.startsWith("file://"))
+ {
+ ref = ref.substring(7);
+ }
+ setSpeciesAndAssembly(ref);
+
+ SequenceI seq = null;
+ File dbFile = new File(ref);
+
+ if (dbFile.exists())
+ {
+ HtsContigDb db = new HtsContigDb("", dbFile);
+ seq = db.getSequenceProxy(contig);
+ loadSequenceVCF(seq);
+ db.close();
+ }
+ else
{
- // long start = System.currentTimeMillis();
- reader = new VCFReader(filePath);
+ Cache.error("VCF reference not found: " + ref);
+ }
+
+ return seq;
+ }
- VCFHeader header = reader.getFileHeader();
+ /**
+ * 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);
- // check if reference is wrt assembly19 (GRCh37)
- // todo may need to allow user to specify reference assembly?
- boolean isRefGrch37 = (ref != null && ref.getValue().contains(
- "assembly19"));
+ String reference = ref == null ? null : ref.getValue();
+
+ setSpeciesAndAssembly(reference);
int varCount = 0;
int seqCount = 0;
@@ -98,9 +365,9 @@ public class VCFLoader
/*
* query for VCF overlapping each sequence in turn
*/
- for (SequenceI seq : al.getSequences())
+ for (SequenceI seq : seqs)
{
- int added = loadVCF(seq, reader, isRefGrch37);
+ int added = loadSequenceVCF(seq);
if (added > 0)
{
seqCount++;
@@ -108,17 +375,24 @@ public class VCFLoader
transferAddedFeatures(seq);
}
}
- // long elapsed = System.currentTimeMillis() - start;
- String msg = String.format("Added %d VCF variants to %d sequence(s)",
- varCount, seqCount);
- if (status != null)
+ if (gui != null)
{
- status.setStatus(msg);
+ String msg = MessageManager.formatMessage("label.added_vcf",
+ varCount, seqCount);
+ gui.setStatus(msg);
+ if (gui.getFeatureSettingsUI() != null)
+ {
+ gui.getFeatureSettingsUI().discoverAllFeatureData();
+ }
}
} catch (Throwable e)
{
System.err.println("Error processing VCF: " + e.getMessage());
e.printStackTrace();
+ if (gui != null)
+ {
+ gui.setStatus("Error occurred - see console for details");
+ }
} finally
{
if (reader != null)
@@ -131,52 +405,70 @@ public class VCFLoader
// ignore
}
}
+ header = null;
+ dictionary = null;
}
}
/**
- * Transfers VCF features to sequences to which this sequence has a mapping.
- * If the mapping is 1:3, computes peptide variants from nucleotide variants.
+ * 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 seq
+ * @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 transferAddedFeatures(SequenceI seq)
+ protected void setSpeciesAndAssembly(String reference)
{
- DBRefEntry[] dbrefs = seq.getDBRefs();
- if (dbrefs == null)
+ if (reference == null)
{
- return;
+ Cache.error("No VCF ##reference found, defaulting to "
+ + DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES);
+ reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified
}
- for (DBRefEntry dbref : dbrefs)
+ reference = reference.toLowerCase(Locale.ROOT);
+
+ /*
+ * 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(","))
{
- Mapping mapping = dbref.getMap();
- if (mapping == null || mapping.getTo() == null)
+ String[] tokens = token.split("=");
+ if (tokens.length == 2)
{
- continue;
+ if (reference.contains(tokens[0].trim().toLowerCase(Locale.ROOT)))
+ {
+ vcfAssembly = tokens[1].trim();
+ break;
+ }
}
+ }
- SequenceI mapTo = mapping.getTo();
- MapList map = mapping.getMap();
- if (map.getFromRatio() == 3)
- {
- /*
- * dna-to-peptide product mapping
- */
- AlignmentUtils.computeProteinFeatures(seq, mapTo, map);
- }
- else
+ vcfSpecies = DEFAULT_SPECIES;
+ prop = Cache.getProperty(VCF_SPECIES);
+ if (prop != null)
+ {
+ for (String token : prop.split(","))
{
- /*
- * nucleotide-to-nucleotide mapping e.g. transcript to CDS
- */
- // TODO no DBRef to CDS is added to transcripts
- List features = seq.getFeatures()
- .getPositionalFeatures(SequenceOntologyI.SEQUENCE_VARIANT);
- for (SequenceFeature sf : features)
+ String[] tokens = token.split("=");
+ if (tokens.length == 2)
{
- if (FEATURE_GROUP_VCF.equals(sf.getFeatureGroup()))
+ if (reference.contains(tokens[0].trim().toLowerCase(Locale.ROOT)))
{
- transferFeature(sf, mapTo, map);
+ vcfSpecies = tokens[1].trim();
+ break;
}
}
}
@@ -184,218 +476,1023 @@ public class VCFLoader
}
/**
- * Tries to add overlapping variants read from a VCF file to the given
- * sequence, and returns the number of overlapping variants found. Note that
- * this requires the sequence to hold information as to its chromosomal
- * positions and reference, in order to be able to map the VCF variants to the
- * sequence.
+ * Opens the VCF file and parses header data
*
- * @param seq
- * @param reader
- * @param isVcfRefGrch37
- * @return
+ * @param filePath
+ * @throws IOException
*/
- protected int loadVCF(SequenceI seq, VCFReader reader,
- boolean isVcfRefGrch37)
+ private void initialise(String filePath) throws IOException
{
- int count = 0;
- GeneLoci seqCoords = seq.getGeneLoci();
- if (seqCoords == null)
- {
- return 0;
- }
+ vcfFilePath = filePath;
+
+ reader = new VCFReader(filePath);
- List seqChromosomalContigs = seqCoords.mapping.getToRanges();
- for (int[] range : seqChromosomalContigs)
+ header = reader.getFileHeader();
+
+ try
{
- count += addVcfVariants(seq, reader, range, isVcfRefGrch37);
+ dictionary = header.getSequenceDictionary();
+ } catch (SAMException e)
+ {
+ // ignore - thrown if any contig line lacks length info
}
- return count;
+ sourceId = filePath;
+
+ saveMetadata(sourceId);
+
+ /*
+ * get offset of CSQ ALLELE_NUM and Feature if declared
+ */
+ parseCsqHeader();
}
/**
- * 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.
+ * Reads metadata (such as INFO field descriptions and datatypes) and saves
+ * them for future reference
*
- * @param seq
- * @param reader
- * @param range
- * start-end range of a sequence region in its chromosomal
- * coordinates
- * @param isVcfRefGrch37
- * true if the VCF is with reference to GRCh37
- * @return
+ * @param theSourceId
*/
- protected int addVcfVariants(SequenceI seq, VCFReader reader,
- int[] range, boolean isVcfRefGrch37)
+ void saveMetadata(String theSourceId)
{
- GeneLoci seqCoords = seq.getGeneLoci();
+ List vcfFieldPatterns = getFieldMatchers(VCF_FIELDS_PREF,
+ DEFAULT_VCF_FIELDS);
+ vcfFieldsOfInterest = new ArrayList<>();
- String chromosome = seqCoords.chromosome;
- String seqRef = seqCoords.assembly;
- String species = seqCoords.species;
+ FeatureSource metadata = new FeatureSource(theSourceId);
- // TODO handle species properly
- if ("".equals(species))
+ for (VCFInfoHeaderLine info : header.getInfoHeaderLines())
{
- species = "human";
- }
-
- /*
- * map chromosomal coordinates from GRCh38 (sequence) to
- * GRCh37 (VCF) if necessary
- */
- // TODO generalise for other assemblies and species
- int offset = 0;
- String fromRef = "GRCh38";
- if (fromRef.equalsIgnoreCase(seqRef) && isVcfRefGrch37)
- {
- String toRef = "GRCh37";
- int[] newRange = mapReferenceRange(range, chromosome, species,
- fromRef, toRef);
- if (newRange == null)
+ String attributeId = info.getID();
+ String desc = info.getDescription();
+ VCFHeaderLineType type = info.getType();
+ FeatureAttributeType attType = null;
+ switch (type)
{
- System.err.println(String.format(
- "Failed to map %s:%s:%s:%d:%d to %s", species, chromosome,
- fromRef, range[0], range[1], toRef));
- return 0;
+ case Character:
+ attType = FeatureAttributeType.Character;
+ break;
+ case Flag:
+ attType = FeatureAttributeType.Flag;
+ break;
+ case Float:
+ attType = FeatureAttributeType.Float;
+ break;
+ case Integer:
+ attType = FeatureAttributeType.Integer;
+ break;
+ case String:
+ attType = FeatureAttributeType.String;
+ break;
}
- offset = newRange[0] - range[0];
- range = newRange;
- }
-
- boolean forwardStrand = range[0] <= range[1];
-
- /*
- * query the VCF for overlaps
- * (convert a reverse strand range to forwards)
- */
- int count = 0;
- MapList mapping = seqCoords.mapping;
-
- 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())
- {
- /*
- * get variant location in sequence chromosomal coordinates
- */
- VariantContext variant = variants.next();
+ metadata.setAttributeName(attributeId, desc);
+ metadata.setAttributeType(attributeId, attType);
- /*
- * we can only process SNP variants (which can be reported
- * as part of a MIXED variant record
- */
- if (!variant.isSNP() && !variant.isMixed())
+ if (isFieldWanted(attributeId, vcfFieldPatterns))
{
- continue;
+ vcfFieldsOfInterest.add(attributeId);
}
+ }
- count++;
- int start = variant.getStart() - offset;
- int end = variant.getEnd() - offset;
+ FeatureSources.getInstance().addSource(theSourceId, metadata);
+ }
- /*
- * convert chromosomal location to sequence coordinates
- * - null if a partially overlapping feature
- */
- int[] seqLocation = mapping.locateInFrom(start, end);
- if (seqLocation != null)
+ /**
+ * Answers true if the field id is matched by any of the filter patterns, else
+ * false. Matching is against regular expression patterns, and is not
+ * case-sensitive.
+ *
+ * @param id
+ * @param filters
+ * @return
+ */
+ private boolean isFieldWanted(String id, List filters)
+ {
+ for (Pattern p : filters)
+ {
+ if (p.matcher(id.toUpperCase(Locale.ROOT)).matches())
{
- addVariantFeatures(seq, variant, seqLocation[0], seqLocation[1],
- forwardStrand);
+ return true;
}
}
-
- variants.close();
-
- return count;
+ return false;
}
/**
- * Inspects the VCF variant record, and adds variant features to the sequence.
- * Only SNP variants are added, not INDELs.
+ * Records 'wanted' fields defined in the CSQ INFO header (if there is one).
+ * Also records the position of selected fields (Allele, ALLELE_NUM, Feature)
+ * required for processing.
*
- * If the sequence maps to the reverse strand of the chromosome, reference and
- * variant bases are recorded as their complements (C/G, A/T).
- *
- * @param seq
- * @param variant
- * @param featureStart
- * @param featureEnd
- * @param forwardStrand
+ * CSQ fields are declared in the CSQ INFO Description e.g.
+ *
+ * Description="Consequence ...from ... VEP. Format: Allele|Consequence|...
*/
- protected void addVariantFeatures(SequenceI seq, VariantContext variant,
- int featureStart, int featureEnd, boolean forwardStrand)
+ protected void parseCsqHeader()
{
- byte[] reference = variant.getReference().getBases();
- if (reference.length != 1)
+ List vepFieldFilters = getFieldMatchers(VEP_FIELDS_PREF,
+ DEFAULT_VEP_FIELDS);
+ vepFieldsOfInterest = new HashMap<>();
+
+ VCFInfoHeaderLine csqInfo = header.getInfoHeaderLine(CSQ_FIELD);
+ if (csqInfo == null)
{
- /*
- * sorry, we don't handle INDEL variants
- */
return;
}
/*
- * for now we extract allele frequency as feature score; note
- * this attribute is String for a simple SNP, but List if
- * multiple alleles at the locus; we extract for the simple case only
+ * parse out the pipe-separated list of CSQ fields; we assume here that
+ * these form the last part of the description, and contain no spaces
*/
- Object af = variant.getAttribute("AF");
- float score = 0f;
- if (af instanceof String)
- {
- try
- {
- score = Float.parseFloat((String) af);
- } catch (NumberFormatException e)
- {
- // leave as 0
- }
- }
-
- StringBuilder sb = new StringBuilder();
- sb.append(forwardStrand ? (char) reference[0] : complement(reference));
+ String desc = csqInfo.getDescription();
+ int spacePos = desc.lastIndexOf(" ");
+ desc = desc.substring(spacePos + 1);
- /*
- * inspect alleles and record SNP variants (as the variant
- * record could be MIXED and include INDEL and SNP alleles)
- * warning: getAlleles gives no guarantee as to the order
- * in which they are returned
- */
- for (Allele allele : variant.getAlleles())
+ if (desc != null)
{
- if (!allele.isReference())
+ String[] format = desc.split(PIPE_REGEX);
+ int index = 0;
+ for (String field : format)
{
- byte[] alleleBase = allele.getBases();
- if (alleleBase.length == 1)
+ if (CSQ_CONSEQUENCE_KEY.equals(field))
+ {
+ csqConsequenceFieldIndex = index;
+ }
+ if (CSQ_ALLELE_NUM_KEY.equals(field))
+ {
+ csqAlleleNumberFieldIndex = index;
+ }
+ if (CSQ_ALLELE_KEY.equals(field))
+ {
+ csqAlleleFieldIndex = index;
+ }
+ if (CSQ_FEATURE_KEY.equals(field))
+ {
+ csqFeatureFieldIndex = index;
+ }
+
+ if (isFieldWanted(field, vepFieldFilters))
{
- sb.append(",").append(
- forwardStrand ? (char) alleleBase[0]
- : complement(alleleBase));
+ vepFieldsOfInterest.put(index, field);
}
+
+ index++;
}
}
- String alleles = sb.toString(); // e.g. G,A,C
+ }
+ /**
+ * Reads the Preference value for the given key, with default specified if no
+ * preference set. The value is interpreted as a comma-separated list of
+ * regular expressions, and converted into a list of compiled patterns ready
+ * for matching. Patterns are forced to upper-case for non-case-sensitive
+ * matching.
+ *
+ * This supports user-defined filters for fields of interest to capture while
+ * processing data. For example, VCF_FIELDS = AF,AC* would mean that VCF INFO
+ * fields with an ID of AF, or starting with AC, would be matched.
+ *
+ * @param key
+ * @param def
+ * @return
+ */
+ private List getFieldMatchers(String key, String def)
+ {
+ String pref = Cache.getDefault(key, def);
+ List patterns = new ArrayList<>();
+ String[] tokens = pref.split(",");
+ for (String token : tokens)
+ {
+ try
+ {
+ patterns.add(Pattern.compile(token.toUpperCase(Locale.ROOT)));
+ } catch (PatternSyntaxException e)
+ {
+ System.err.println("Invalid pattern ignored: " + token);
+ }
+ }
+ return patterns;
+ }
+
+ /**
+ * Transfers VCF features to sequences to which this sequence has a mapping.
+ *
+ * @param seq
+ */
+ protected void transferAddedFeatures(SequenceI seq)
+ {
+ List dbrefs = seq.getDBRefs();
+ if (dbrefs == null)
+ {
+ return;
+ }
+ for (DBRefEntry dbref : dbrefs)
+ {
+ Mapping mapping = dbref.getMap();
+ if (mapping == null || mapping.getTo() == null)
+ {
+ continue;
+ }
+
+ SequenceI mapTo = mapping.getTo();
+ MapList map = mapping.getMap();
+ if (map.getFromRatio() == 3)
+ {
+ /*
+ * dna-to-peptide product mapping
+ */
+ // JAL-3187 render on the fly instead
+ // AlignmentUtils.computeProteinFeatures(seq, mapTo, map);
+ }
+ else
+ {
+ /*
+ * nucleotide-to-nucleotide mapping e.g. transcript to CDS
+ */
+ List features = seq.getFeatures()
+ .getPositionalFeatures(SequenceOntologyI.SEQUENCE_VARIANT);
+ for (SequenceFeature sf : features)
+ {
+ if (FEATURE_GROUP_VCF.equals(sf.getFeatureGroup()))
+ {
+ transferFeature(sf, mapTo, map);
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Tries to add overlapping variants read from a VCF file to the given sequence,
+ * and returns the number of variant features added
+ *
+ * @param seq
+ * @return
+ */
+ protected int loadSequenceVCF(SequenceI seq)
+ {
+ VCFMap vcfMap = getVcfMap(seq);
+ if (vcfMap == null)
+ {
+ return 0;
+ }
+
+ /*
+ * work with the dataset sequence here
+ */
+ SequenceI dss = seq.getDatasetSequence();
+ if (dss == null)
+ {
+ dss = seq;
+ }
+ return addVcfVariants(dss, vcfMap);
+ }
+
+ /**
+ * Answers a map from sequence coordinates to VCF chromosome ranges
+ *
+ * @param seq
+ * @return
+ */
+ private VCFMap getVcfMap(SequenceI seq)
+ {
+ /*
+ * simplest case: sequence has id and length matching a VCF contig
+ */
+ VCFMap vcfMap = null;
+ if (dictionary != null)
+ {
+ vcfMap = getContigMap(seq);
+ }
+ if (vcfMap != null)
+ {
+ return vcfMap;
+ }
+
+ /*
+ * otherwise, map to VCF from chromosomal coordinates
+ * of the sequence (if known)
+ */
+ GeneLociI seqCoords = seq.getGeneLoci();
+ if (seqCoords == null)
+ {
+ Cache.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();
+ MapList map = seqCoords.getMapping();
+
+ // note this requires the configured species to match that
+ // returned with the Ensembl sequence; todo: support aliases?
+ if (!vcfSpecies.equalsIgnoreCase(species))
+ {
+ Cache.warn("No VCF loaded to " + seq.getName()
+ + " as species not matched");
+ return null;
+ }
+
+ if (seqRef.equalsIgnoreCase(vcfAssembly))
+ {
+ return new VCFMap(chromosome, map);
+ }
+
+ /*
+ * VCF data has a different reference assembly to the sequence:
+ * query Ensembl to map chromosomal coordinates from sequence to VCF
+ */
+ List toVcfRanges = new ArrayList<>();
+ List fromSequenceRanges = new ArrayList<>();
+
+ for (int[] range : map.getToRanges())
+ {
+ int[] fromRange = map.locateInFrom(range[0], range[1]);
+ if (fromRange == null)
+ {
+ // corrupted map?!?
+ continue;
+ }
+
+ int[] newRange = mapReferenceRange(range, chromosome, "human", seqRef,
+ vcfAssembly);
+ if (newRange == null)
+ {
+ Cache.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);
+ }
+ }
+
+ return new VCFMap(chromosome,
+ new MapList(fromSequenceRanges, toVcfRanges, 1, 1));
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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 seq
+ * @param map
+ * mapping from sequence to VCF coordinates
+ * @return
+ */
+ protected int addVcfVariants(SequenceI seq, VCFMap map)
+ {
+ 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
+ {
+ CloseableIterator variants = reader
+ .query(map.chromosome, vcfStart, vcfEnd);
+ while (variants.hasNext())
+ {
+ VariantContext variant = variants.next();
+
+ int[] featureRange = map.map.locateInFrom(variant.getStart(),
+ variant.getEnd());
+
+ /*
+ * only take features whose range is fully mappable to sequence positions
+ */
+ if (featureRange != null)
+ {
+ int featureStart = Math.min(featureRange[0], featureRange[1]);
+ int featureEnd = Math.max(featureRange[0], featureRange[1]);
+ if (featureEnd - featureStart == variant.getEnd()
+ - variant.getStart())
+ {
+ count += addAlleleFeatures(seq, variant, featureStart,
+ featureEnd, forwardStrand);
+ }
+ }
+ }
+ variants.close();
+ } catch (TribbleException e)
+ {
+ /*
+ * RuntimeException throwable by htsjdk
+ */
+ String msg = String.format("Error reading VCF for %s:%d-%d: %s ",
+ map.chromosome, vcfStart, vcfEnd,e.getLocalizedMessage());
+ Cache.error(msg);
+ }
+ }
+
+ return count;
+ }
+
+ /**
+ * A convenience method to get an attribute value for an alternate allele
+ *
+ * @param variant
+ * @param attributeName
+ * @param alleleIndex
+ * @return
+ */
+ protected String getAttributeValue(VariantContext variant,
+ String attributeName, int alleleIndex)
+ {
+ Object att = variant.getAttribute(attributeName);
+
+ if (att instanceof String)
+ {
+ return (String) att;
+ }
+ else if (att instanceof ArrayList)
+ {
+ return ((List) att).get(alleleIndex);
+ }
+
+ return null;
+ }
+
+ /**
+ * Adds one variant feature for each allele in the VCF variant record, and
+ * returns the number of features added.
+ *
+ * @param seq
+ * @param variant
+ * @param featureStart
+ * @param featureEnd
+ * @param forwardStrand
+ * @return
+ */
+ protected int addAlleleFeatures(SequenceI seq, VariantContext variant,
+ int featureStart, int featureEnd, boolean forwardStrand)
+ {
+ int added = 0;
+
+ /*
+ * Javadoc says getAlternateAlleles() imposes no order on the list returned
+ * so we proceed defensively to get them in strict order
+ */
+ int altAlleleCount = variant.getAlternateAlleles().size();
+ for (int i = 0; i < altAlleleCount; i++)
+ {
+ added += addAlleleFeature(seq, variant, i, featureStart, featureEnd,
+ forwardStrand);
+ }
+ return added;
+ }
+
+ /**
+ * Inspects one allele and attempts to add a variant feature for it to the
+ * 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
+ * @param altAlleleIndex
+ * (0, 1..)
+ * @param featureStart
+ * @param featureEnd
+ * @param forwardStrand
+ * @return
+ */
+ protected int addAlleleFeature(SequenceI seq, VariantContext variant,
+ int altAlleleIndex, int featureStart, int featureEnd,
+ boolean forwardStrand)
+ {
+ String reference = variant.getReference().getBaseString();
+ Allele alt = variant.getAlternateAllele(altAlleleIndex);
+ 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
+ */
+ 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(Locale.ROOT),
+ csqFeatureFieldIndex);
+
+ /*
+ * pick out the ontology term for the consequence type
+ */
String type = SequenceOntologyI.SEQUENCE_VARIANT;
+ 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);
+
+ /*
+ * save the derived alleles as a named attribute; this will be
+ * needed when Jalview computes derived peptide variants
+ */
+ addFeatureAttribute(sf, Gff3Helper.ALLELES, alleles);
+
+ /*
+ * 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);
+
+ return 1;
+ }
+
+ /**
+ * 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;
- sf.setValue(Gff3Helper.ALLELES, alleles);
+ /*
+ * 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(Locale.ROOT)) > -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 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,
+ SequenceFeature sf, final int altAlelleIndex, String consequence)
+ {
Map atts = variant.getAttributes();
+
for (Entry att : atts.entrySet())
{
- sf.setValue(att.getKey(), att.getValue());
+ String key = att.getKey();
+
+ /*
+ * extract Consequence data (if present) that we are able to
+ * associated with the allele for this variant feature
+ */
+ if (CSQ_FIELD.equals(key))
+ {
+ addConsequences(variant, sf, consequence);
+ continue;
+ }
+
+ /*
+ * filter out fields we don't want to capture
+ */
+ if (!vcfFieldsOfInterest.contains(key))
+ {
+ continue;
+ }
+
+ /*
+ * we extract values for other data which are allele-specific;
+ * these may be per alternate allele (INFO[key].Number = 'A')
+ * or per allele including reference (INFO[key].Number = 'R')
+ */
+ VCFInfoHeaderLine infoHeader = header.getInfoHeaderLine(key);
+ if (infoHeader == null)
+ {
+ /*
+ * can't be sure what data belongs to this allele, so
+ * play safe and don't take any
+ */
+ continue;
+ }
+
+ VCFHeaderLineCount number = infoHeader.getCountType();
+ int index = altAlelleIndex;
+ if (number == VCFHeaderLineCount.R)
+ {
+ /*
+ * one value per allele including reference, so bump index
+ * e.g. the 3rd value is for the 2nd alternate allele
+ */
+ index++;
+ }
+ else if (number != VCFHeaderLineCount.A)
+ {
+ /*
+ * don't save other values as not allele-related
+ */
+ continue;
+ }
+
+ /*
+ * take the index'th value
+ */
+ String value = getAttributeValue(variant, key, index);
+ 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.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)
+ {
+ 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.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.
+ *
+ * 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 sf
+ * @param myConsequence
+ */
+ protected void addConsequences(VariantContext variant, SequenceFeature sf,
+ String myConsequence)
+ {
+ Object value = variant.getAttribute(CSQ_FIELD);
+
+ if (value == null || !(value instanceof List))
+ {
+ return;
+ }
+
+ List consequences = (List) value;
+
+ /*
+ * inspect CSQ consequences; restrict to the consequence
+ * associated with the current transcript (Feature)
+ */
+ Map csqValues = new HashMap<>();
+
+ for (String consequence : consequences)
+ {
+ 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'
+ */
+ int i = 0;
+ for (String field : csqFields)
+ {
+ if (field != null && field.length() > 0)
+ {
+ 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);
+ }
+ }
+ i++;
+ }
+ }
+ }
+
+ if (!csqValues.isEmpty())
+ {
+ sf.setValue(CSQ_FIELD, csqValues);
}
- seq.addSequenceFeature(sf);
}
/**
@@ -449,8 +1546,8 @@ public class VCFLoader
* call (e.g.) http://rest.ensembl.org/map/human/GRCh38/17:45051610..45109016:1/GRCh37
*/
EnsemblMap mapper = new EnsemblMap();
- int[] mapping = mapper.getMapping(species, chromosome, fromRef, toRef,
- queryRange);
+ int[] mapping = mapper.getAssemblyMapping(species, chromosome, fromRef,
+ toRef, queryRange);
if (mapping == null)
{