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;
}
