+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.io.vcf;
-import jalview.analysis.AlignmentUtils;
-import jalview.analysis.Dna;
-import jalview.api.AlignViewControllerGuiI;
-import jalview.bin.Cache;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.GeneLociI;
-import jalview.datamodel.Mapping;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.FeatureAttributeType;
-import jalview.datamodel.features.FeatureSource;
-import jalview.datamodel.features.FeatureSources;
-import jalview.ext.ensembl.EnsemblMap;
-import jalview.ext.htsjdk.HtsContigDb;
-import jalview.ext.htsjdk.VCFReader;
-import jalview.io.gff.Gff3Helper;
-import jalview.io.gff.SequenceOntologyI;
-import jalview.util.MapList;
-import jalview.util.MappingUtils;
-import jalview.util.MessageManager;
-
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import htsjdk.variant.vcf.VCFHeaderLineCount;
import htsjdk.variant.vcf.VCFHeaderLineType;
import htsjdk.variant.vcf.VCFInfoHeaderLine;
+import jalview.analysis.Dna;
+import jalview.api.AlignViewControllerGuiI;
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLociI;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureAttributeType;
+import jalview.datamodel.features.FeatureSource;
+import jalview.datamodel.features.FeatureSources;
+import jalview.ext.ensembl.EnsemblMap;
+import jalview.ext.htsjdk.HtsContigDb;
+import jalview.ext.htsjdk.VCFReader;
+import jalview.io.gff.Gff3Helper;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+import jalview.util.StringUtils;
/**
* A class to read VCF data (using the htsjdk) and add variants as sequence
*/
public class VCFLoader
{
+ private static final String VCF_ENCODABLE = ":;=%,";
+
+ /*
+ * Jalview feature attributes for VCF fixed column data
+ */
+ private static final String VCF_POS = "POS";
+
+ private static final String VCF_ID = "ID";
+
+ private static final String VCF_QUAL = "QUAL";
+
+ private static final String VCF_FILTER = "FILTER";
+
private static final String NO_VALUE = VCFConstants.MISSING_VALUE_v4; // '.'
private static final String DEFAULT_SPECIES = "homo_sapiens";
/**
* Transfers VCF features to sequences to which this sequence has a mapping.
- * If the mapping is 3:1, computes peptide variants from nucleotide variants.
*
* @param seq
*/
protected void transferAddedFeatures(SequenceI seq)
{
- DBRefEntry[] dbrefs = seq.getDBRefs();
+ List<DBRefEntry> dbrefs = seq.getDBRefs();
if (dbrefs == null)
{
return;
/*
* dna-to-peptide product mapping
*/
- AlignmentUtils.computeProteinFeatures(seq, mapTo, map);
+ // JAL-3187 render on the fly instead
+ // AlignmentUtils.computeProteinFeatures(seq, mapTo, map);
}
else
{
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]);
- count += addAlleleFeatures(seq, variant, featureStart,
- featureEnd, forwardStrand);
+ if (featureEnd - featureStart == variant.getEnd()
+ - variant.getStart())
+ {
+ count += addAlleleFeatures(seq, variant, featureStart,
+ featureEnd, forwardStrand);
+ }
}
}
variants.close();
* RuntimeException throwable by htsjdk
*/
String msg = String.format("Error reading VCF for %s:%d-%d: %s ",
- map.chromosome, vcfStart, vcfEnd);
+ map.chromosome, vcfStart, vcfEnd,e.getLocalizedMessage());
Cache.log.error(msg);
}
}
if (att instanceof String)
{
- return NO_VALUE.equals(att) ? null : (String) att;
+ return (String) att;
}
else if (att instanceof ArrayList)
{
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);
+
+ /*
+ * 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);
}
/**
+ * 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<String> filters = variant.getFilters();
+ if (filters.isEmpty())
+ {
+ return NO_VALUE;
+ }
+ Iterator<String> 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:
}
/*
- * 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')
String value = getAttributeValue(variant, key, index);
if (value != null && isValid(variant, key, value))
{
- sf.setValue(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);
}
}
}
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);
}
}
git://source.jalview.org / jalview.git / blobdiff