import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
-import java.util.SortedMap;
-import java.util.TreeMap;
import java.util.regex.Pattern;
import java.util.regex.PatternSyntaxException;
+import htsjdk.samtools.SAMException;
+import htsjdk.samtools.SAMSequenceDictionary;
+import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.VariantContext;
*/
public class VCFLoader
{
+ /**
+ * A class to model the mapping from sequence to VCF coordinates. Cases include
+ * <ul>
+ * <li>a direct 1:1 mapping where the sequence is one of the VCF contigs</li>
+ * <li>a mapping of sequence to chromosomal coordinates, where sequence and VCF
+ * use the same reference assembly</li>
+ * <li>a modified mapping of sequence to chromosomal coordinates, where sequence
+ * and VCF use different reference assembles</li>
+ * </ul>
+ */
+ class VCFMap
+ {
+ final String chromosome;
+
+ final MapList map;
+
+ VCFMap(String chr, MapList m)
+ {
+ chromosome = chr;
+ map = m;
+ }
+
+ @Override
+ public String toString()
+ {
+ return chromosome + ":" + map.toString();
+ }
+ }
+
/*
* Lookup keys, and default values, for Preference entries that describe
* patterns for VCF and VEP fields to capture
* keys to fields of VEP CSQ consequence data
* see https://www.ensembl.org/info/docs/tools/vep/vep_formats.html
*/
- private static final String ALLELE_KEY = "Allele";
-
- private static final String ALLELE_NUM_KEY = "ALLELE_NUM"; // 0 (ref), 1...
- private static final String FEATURE_KEY = "Feature"; // Ensembl stable id
+ private static final String CSQ_CONSEQUENCE_KEY = "Consequence";
+ private static final String CSQ_ALLELE_KEY = "Allele";
+ private static final String CSQ_ALLELE_NUM_KEY = "ALLELE_NUM"; // 0 (ref), 1...
+ private static final String CSQ_FEATURE_KEY = "Feature"; // Ensembl stable id
/*
* default VCF INFO key for VEP consequence data
private VCFHeader header;
/*
+ * a Dictionary of contigs (if present) referenced in the VCF file
+ */
+ private SAMSequenceDictionary dictionary;
+
+ /*
* the position (0...) of field in each block of
* CSQ (consequence) data (if declared in the VCF INFO header for CSQ)
* see http://www.ensembl.org/info/docs/tools/vep/vep_formats.html
*/
+ private int csqConsequenceFieldIndex = -1;
private int csqAlleleFieldIndex = -1;
private int csqAlleleNumberFieldIndex = -1;
private int csqFeatureFieldIndex = -1;
+ // todo the same fields for SnpEff ANN data if wanted
+ // see http://snpeff.sourceforge.net/SnpEff_manual.html#input
+
/*
* a unique identifier under which to save metadata about feature
* attributes (selected INFO field data)
header = reader.getFileHeader();
+ try
+ {
+ dictionary = header.getSequenceDictionary();
+ } catch (SAMException e)
+ {
+ // ignore - thrown if any contig line lacks length info
+ }
+
sourceId = filePath;
saveMetadata(sourceId);
// ignore
}
}
+ header = null;
+ dictionary = null;
}
}
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;
}
protected int loadSequenceVCF(SequenceI seq, VCFReader reader,
String vcfAssembly)
{
- int count = 0;
+ VCFMap vcfMap = getVcfMap(seq, vcfAssembly);
+ if (vcfMap == null)
+ {
+ return 0;
+ }
+
+ return addVcfVariants(seq, reader, vcfMap, vcfAssembly);
+ }
+
+ /**
+ * Answers a map from sequence coordinates to VCF chromosome ranges
+ *
+ * @param seq
+ * @param vcfAssembly
+ * @return
+ */
+ private VCFMap getVcfMap(SequenceI seq, String vcfAssembly)
+ {
+ /*
+ * 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)
{
- System.out.println(String.format(
+ Cache.log.warn(String.format(
"Can't query VCF for %s as chromosome coordinates not known",
seq.getName()));
- return 0;
+ return null;
}
- if (!vcfSpeciesMatchesSequence(vcfAssembly, seqCoords.getSpeciesId()))
+ String species = seqCoords.getSpeciesId();
+ String chromosome = seqCoords.getChromosomeId();
+ String seqRef = seqCoords.getAssemblyId();
+ MapList map = seqCoords.getMap();
+
+ if (!vcfSpeciesMatchesSequence(vcfAssembly, species))
{
- return 0;
+ return null;
}
- List<int[]> seqChromosomalContigs = seqCoords.getMap().getToRanges();
- for (int[] range : seqChromosomalContigs)
+ if (vcfAssemblyMatchesSequence(vcfAssembly, seqRef))
{
- count += addVcfVariants(seq, reader, range, vcfAssembly);
+ return new VCFMap(chromosome, map);
}
- return count;
+ if (!"GRCh38".equalsIgnoreCase(seqRef) // Ensembl
+ || !vcfAssembly.contains("Homo_sapiens_assembly19")) // gnomAD
+ {
+ return null;
+ }
+
+ /*
+ * map chromosomal coordinates from sequence to VCF if the VCF
+ * data has a different reference assembly to the sequence
+ */
+ // TODO generalise for cases other than GRCh38 -> GRCh37 !
+ // - or get the user to choose in a dialog
+
+ List<int[]> toVcfRanges = new ArrayList<>();
+ List<int[]> fromSequenceRanges = new ArrayList<>();
+ String toRef = "GRCh37";
+
+ 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,
+ toRef);
+ if (newRange == null)
+ {
+ Cache.log.error(
+ String.format("Failed to map %s:%s:%s:%d:%d to %s", species,
+ chromosome, seqRef, range[0], range[1], toRef));
+ 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;
+ }
+
+ /**
+ * Answers true if we determine that the VCF data uses the same reference
+ * assembly as the sequence, else false
+ *
+ * @param vcfAssembly
+ * @param seqRef
+ * @return
+ */
+ private boolean vcfAssemblyMatchesSequence(String vcfAssembly,
+ String seqRef)
+ {
+ // TODO improve on this stub, which handles gnomAD and
+ // hopes for the best for other cases
+
+ if ("GRCh38".equalsIgnoreCase(seqRef) // Ensembl
+ && vcfAssembly.contains("Homo_sapiens_assembly19")) // gnomAD
+ {
+ return false;
+ }
+ return true;
}
/**
}
/**
- * 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
+ * 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 reader
- * @param range
- * start-end range of a sequence region in its chromosomal
- * coordinates
+ * @param map
+ * mapping from sequence to VCF coordinates
* @param vcfAssembly
* the '##reference' identifier for the VCF reference assembly
* @return
*/
protected int addVcfVariants(SequenceI seq, VCFReader reader,
- int[] range, String vcfAssembly)
+ VCFMap map, String vcfAssembly)
{
- GeneLociI seqCoords = seq.getGeneLoci();
-
- String chromosome = seqCoords.getChromosomeId();
- String seqRef = seqCoords.getAssemblyId();
- String species = seqCoords.getSpeciesId();
-
- /*
- * 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
- {
- 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;
- }
-
- boolean forwardStrand = range[0] <= range[1];
+ boolean forwardStrand = map.map.isToForwardStrand();
/*
- * query the VCF for overlaps
- * (convert a reverse strand range to forwards)
+ * query the VCF for overlaps of each contiguous chromosomal region
*/
int count = 0;
- MapList mapping = seqCoords.getMap();
- int fromLocus = Math.min(range[0], range[1]);
- int toLocus = Math.max(range[0], range[1]);
- CloseableIterator<VariantContext> variants = reader.query(chromosome,
- fromLocus, toLocus);
- while (variants.hasNext())
+ for (int[] range : map.map.getToRanges())
{
- /*
- * get variant location in sequence chromosomal coordinates
- */
- VariantContext variant = variants.next();
+ int vcfStart = Math.min(range[0], range[1]);
+ int vcfEnd = Math.max(range[0], range[1]);
+ CloseableIterator<VariantContext> variants = reader
+ .query(map.chromosome, vcfStart, vcfEnd);
+ while (variants.hasNext())
+ {
+ VariantContext variant = variants.next();
- int start = variant.getStart() - offset;
- int end = variant.getEnd() - offset;
+ int[] featureRange = map.map.locateInFrom(variant.getStart(),
+ variant.getEnd());
- /*
- * 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 featureStart = Math.min(seqLocation[0], seqLocation[1]);
- int featureEnd = Math.max(seqLocation[0], seqLocation[1]);
- count += addAlleleFeatures(seq, variant, featureStart, featureEnd,
- forwardStrand);
+ 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();
}
- variants.close();
-
return count;
}
/**
* 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
* 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
+ // FIXME correctly handle insertions on reverse strand JAL-2845
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
- String type = SequenceOntologyI.SEQUENCE_VARIANT;
+ String type = getOntologyTerm(seq, variant, altAlleleIndex);
+
float score = getAlleleFrequency(variant, altAlleleIndex);
SequenceFeature sf = new SequenceFeature(type, alleles, featureStart,
}
/**
+ * 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:
+ * <ul>
+ * <li>VEP (or SnpEff) Consequence annotation is included in the VCF</li>
+ * <li>sequence id can be matched to VEP Feature (or SnpEff Feature_ID)</li>
+ * </ul>
+ *
+ * @param seq
+ * @param variant
+ * @param altAlleleIndex
+ * @return
+ * @see http://www.sequenceontology.org/browser/current_svn/term/SO:0001060
+ */
+ String getOntologyTerm(SequenceI seq, VariantContext variant,
+ int altAlleleIndex)
+ {
+ String type = SequenceOntologyI.SEQUENCE_VARIANT;
+
+ if (csqAlleleFieldIndex == -1) // && snpEffAlleleFieldIndex == -1
+ {
+ /*
+ * no Consequence data so we can't refine the ontology term
+ */
+ return type;
+ }
+
+ /*
+ * can we associate Consequence data with this allele and feature (transcript)?
+ * if so, prefer the consequence term from that data
+ */
+ String consequence = getConsequenceForAlleleAndFeature(variant,
+ CSQ_FIELD,
+ altAlleleIndex, csqAlleleFieldIndex, csqAlleleNumberFieldIndex,
+ seq.getName().toLowerCase(), csqFeatureFieldIndex);
+ 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.
+ * <ul>
+ * <li>inspects the VCF data for key 'vcfInfoId'</li>
+ * <li>splits this on comma (to distinct consequences)</li>
+ * <li>returns the first consequence (if any) where</li>
+ * <ul>
+ * <li>the allele matches the altAlleleIndex'th allele of variant</li>
+ * <li>the feature matches the sequence name (e.g. transcript id)</li>
+ * </ul>
+ * </ul>
+ * 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<String> consequences = (List<String>) 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 variant
* @param seq
* @param sf
- * @param altAlelleIndex
+ * @param altAlleleIndex
* (0, 1..)
*/
protected void addConsequences(VariantContext variant, SequenceI seq,
- SequenceFeature sf, int altAlelleIndex)
+ SequenceFeature sf, int altAlleleIndex)
{
+ /*
+ * first try to identify the matching consequence
+ */
+ String myConsequence = getConsequenceForAlleleAndFeature(variant,
+ CSQ_FIELD, altAlleleIndex, csqAlleleFieldIndex,
+ csqAlleleNumberFieldIndex, seq.getName().toLowerCase(),
+ csqFeatureFieldIndex);
+
Object value = variant.getAttribute(CSQ_FIELD);
- if (value == null || !(value instanceof ArrayList<?>))
+ if (value == null || !(value instanceof List<?>))
{
return;
}
List<String> consequences = (List<String>) 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<String, String> csqValues = new TreeMap<>(
- String.CASE_INSENSITIVE_ORDER);
+ Map<String, String> 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'
}
/**
- * Answers true if we want to associate this block of consequence data with
- * the specified alternate allele of the VCF variant.
- * <p>
- * 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.
- * <p>
- * 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
*
git://source.jalview.org / jalview.git / commitdiff