package jalview.io.vcf;
-import jalview.analysis.AlignmentUtils;
import jalview.analysis.Dna;
import jalview.api.AlignViewControllerGuiI;
import jalview.bin.Cache;
import java.io.File;
import java.io.IOException;
+import java.io.UnsupportedEncodingException;
+import java.net.URLDecoder;
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;
*/
public class VCFLoader
{
+ private static final String ENCODED_COMMA = "%2C";
+
+ private static final String ENCODED_PERCENT = "%25";
+
+ private static final String ENCODED_EQUALS = "%3D";
+
+ private static final String ENCODED_SEMICOLON = "%3B";
+
+ private static final String ENCODED_COLON = "%3A";
+
+ private static final String UTF_8 = "UTF-8";
+
+ /*
+ * 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";
/*
* dna-to-peptide product mapping
*/
- AlignmentUtils.computeProteinFeatures(seq, mapTo, map);
+ // JAL-3187 render on the fly instead
+ // AlignmentUtils.computeProteinFeatures(seq, mapTo, map);
}
else
{
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);
+ value = decodeSpecialCharacters(value);
+ addFeatureAttribute(sf, key, value);
}
}
}
/**
+ * Decodes colon, semicolon, equals sign, percent sign, comma to their decoded
+ * form. The VCF specification (para 1.2) requires these to be encoded where not
+ * used with their special meaning in the VCF syntax. Note that general URL
+ * decoding should not be applied, since this would incorrectly decode (for
+ * example) a '+' sign.
+ *
+ * @param value
+ * @return
+ */
+ protected static String decodeSpecialCharacters(String value)
+ {
+ /*
+ * avoid regex compilation if it is not needed!
+ */
+ if (!value.contains(ENCODED_COLON) && !value.contains(ENCODED_SEMICOLON)
+ && !value.contains(ENCODED_EQUALS)
+ && !value.contains(ENCODED_PERCENT)
+ && !value.contains(ENCODED_COMMA))
+ {
+ return value;
+ }
+
+ value = value.replace(ENCODED_COLON, ":")
+ .replace(ENCODED_SEMICOLON, ";").replace(ENCODED_EQUALS, "=")
+ .replace(ENCODED_PERCENT, "%").replace(ENCODED_COMMA, ",");
+ return 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.
String id = vepFieldsOfInterest.get(i);
if (id != null)
{
+ /*
+ * VCF spec requires encoding of special characters e.g. '='
+ * so decode them here before storing
+ */
+ try
+ {
+ field = URLDecoder.decode(field, UTF_8);
+ } catch (UnsupportedEncodingException e)
+ {
+ }
csqValues.put(id, field);
}
}
git://source.jalview.org / jalview.git / blobdiff