private static AlleleMapper resolveIncompatibleAlleles(
Allele refAllele, VariantContext vc, Set<Allele> allAlleles) {
if (refAllele.equals(vc.getReference())) return new AlleleMapper(vc);
else {
// we really need to do some work. The refAllele is the longest reference allele seen at this
// start site. So imagine it is:
//
// refAllele: ACGTGA
// myRef: ACGT
// myAlt: -
//
// We need to remap all of the alleles in vc to include the extra GA so that
// myRef => refAllele and myAlt => GA
//
Allele myRef = vc.getReference();
if (refAllele.length() <= myRef.length())
throw new ReviewedStingException(
"BUG: myRef=" + myRef + " is longer than refAllele=" + refAllele);
byte[] extraBases =
Arrays.copyOfRange(refAllele.getBases(), myRef.length(), refAllele.length());
// System.out.printf("Remapping allele at %s%n", vc);
// System.out.printf("ref %s%n", refAllele);
// System.out.printf("myref %s%n", myRef );
// System.out.printf("extrabases %s%n", new String(extraBases));
Map<Allele, Allele> map = new HashMap<Allele, Allele>();
for (Allele a : vc.getAlleles()) {
if (a.isReference()) map.put(a, refAllele);
else {
Allele extended = Allele.extend(a, extraBases);
for (Allele b : allAlleles) if (extended.equals(b)) extended = b;
// System.out.printf(" Extending %s => %s%n", a, extended);
map.put(a, extended);
}
}
// debugging
// System.out.printf("mapping %s%n", map);
return new AlleleMapper(map);
}
}
