private boolean addAnnotationsFromString(VariantRec var, String str)
throws OperationFailedException {
String[] toks = str.split("\t");
if (!toks[0].equals(var.getContig())) {
// We expect that sometimes we'll not get the right contig
return false;
}
if (!toks[1].equals("" + var.getStart())) {
// We expect that sometimes we'll not get the right position (not sure why exactly... tabix
// doesn't work perfectly I guess return;
}
if (toks[4].equals(var.getAlt())) {
String rsNum = toks[2];
var.addAnnotation(VariantRec.RSNUM, rsNum);
return true;
}
return false;
}
/**
* Parses allele frequency annotation from the given string and converts it to a property on the
* variant
*
* @param var
* @param str
* @throws OperationFailedException
*/
@Override
protected boolean addAnnotationsFromString(VariantRec var, String val, int altIndex) {
String[] toks = val.split("\t");
String[] formatToks = toks[7].split(";");
String overallFreqStr = valueForKey(formatToks, "AF=");
if (overallFreqStr != null) {
Double af = Double.parseDouble(overallFreqStr);
var.addProperty(VariantRec.UK10K_ALLELE_FREQ, af);
}
return true;
}
@Override
public void annotateVariant(VariantRec var) throws OperationFailedException {
if (reader == null) {
initializeReader();
}
if (reader == null) {
throw new OperationFailedException("Could not initialize tabix reader", this);
}
String contig = var.getContig();
Integer pos = var.getStart();
String queryStr = contig + ":" + pos + "-" + (pos);
// int count = 0;
try {
TabixReader.Iterator iter = reader.query(queryStr);
if (iter != null) {
try {
String val = iter.next();
while (val != null) {
boolean ok = addAnnotationsFromString(var, val);
if (ok) {
break;
}
val = iter.next();
}
} catch (IOException e) {
throw new OperationFailedException(
"Error reading dbSNP data file: " + e.getMessage(), this);
}
}
} catch (RuntimeException rex) {
// Bad contigs will cause an array out-of-bounds exception to be thrown by
// the tabix reader. There's not much we can do about this since the methods
// are private... right now we just ignore it and skip this variant
}
}
