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;
+import java.util.Set;
import java.util.regex.Pattern;
import java.util.regex.PatternSyntaxException;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.SAMSequenceRecord;
import htsjdk.samtools.util.CloseableIterator;
+import htsjdk.tribble.TribbleException;
import htsjdk.variant.variantcontext.Allele;
import htsjdk.variant.variantcontext.VariantContext;
+import htsjdk.variant.vcf.VCFConstants;
import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLine;
import htsjdk.variant.vcf.VCFHeaderLineCount;
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";
/**
*/
Map<Integer, String> vepFieldsOfInterest;
+ /*
+ * key:value for which rejected data has been seen
+ * (the error is logged only once for each combination)
+ */
+ private Set<String> badData;
+
/**
* Constructor given a VCF file
*
{
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())
+ try
{
- VariantContext variant = variants.next();
+ CloseableIterator<VariantContext> variants = reader
+ .query(map.chromosome, vcfStart, vcfEnd);
+ while (variants.hasNext())
+ {
+ VariantContext variant = variants.next();
- int[] featureRange = map.map.locateInFrom(variant.getStart(),
- variant.getEnd());
+ 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);
+ 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)
+ {
+ /*
+ * RuntimeException throwable by htsjdk
+ */
+ String msg = String.format("Error reading VCF for %s:%d-%d: %s ",
+ map.chromosome, vcfStart, vcfEnd);
+ Cache.log.error(msg);
}
- variants.close();
}
return count;
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:
* take the index'th value
*/
String value = getAttributeValue(variant, key, index);
- if (value != null)
+ if (value != null && isValid(variant, key, value))
{
value = decodeSpecialCharacters(value);
- sf.setValue(key, value);
+ 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)
+ {
+ 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.
* <p>
git://source.jalview.org / jalview.git / blobdiff