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:
@@ -1209,14 +1321,6 @@ public class VCFLoader
}
/*
- * 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')
@@ -1241,6 +1345,10 @@ public class VCFLoader
*/
index++;
}
+ else if (number == VCFHeaderLineCount.UNBOUNDED) // .
+ {
+ index = -1;
+ }
else if (number != VCFHeaderLineCount.A)
{
/*
@@ -1253,14 +1361,85 @@ public class VCFLoader
* take the index'th value
*/
String value = getAttributeValue(variant, key, index);
- if (value != null)
+ 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);
}
}
}
/**
+ * 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.
*
@@ -1308,6 +1487,11 @@ public class VCFLoader
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);
}
}