// protected basic manipulation routines
private static List<Allele> makeAlleles(Collection<Allele> alleles) {
final List<Allele> alleleList = new ArrayList<Allele>(alleles.size());
boolean sawRef = false;
for (final Allele a : alleles) {
for (final Allele b : alleleList) {
if (a.equals(b, true))
throw new IllegalArgumentException("Duplicate allele added to VariantContext: " + a);
}
// deal with the case where the first allele isn't the reference
if (a.isReference()) {
if (sawRef)
throw new IllegalArgumentException(
"Alleles for a VariantContext must contain at most one reference allele: " + alleles);
alleleList.add(0, a);
sawRef = true;
} else alleleList.add(a);
}
if (alleleList.isEmpty())
throw new IllegalArgumentException(
"Cannot create a VariantContext with an empty allele list");
if (alleleList.get(0).isNonReference())
throw new IllegalArgumentException(
"Alleles for a VariantContext must contain at least one reference allele: " + alleles);
return alleleList;
}
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);
}
}
public boolean hasAllele(Allele allele, boolean ignoreRefState) {
if (allele == REF || allele == ALT) // optimization for cached cases
return true;
for (Allele a : getAlleles()) {
if (a.equals(allele, ignoreRefState)) return true;
}
return false;
}
public int[] getGLIndecesOfAlternateAllele(Allele targetAllele) {
int index = 1;
for (Allele allele : getAlternateAlleles()) {
if (allele.equals(targetAllele)) break;
index++;
}
return GenotypeLikelihoods.getPLIndecesOfAlleles(0, index);
}
static boolean doubleAllelesSegregatePerfectlyAmongSamples(
VariantContext vc1, VariantContext vc2) {
// Check that Alleles at vc1 and at vc2 always segregate together in all samples (including
// reference):
Map<Allele, Allele> allele1ToAllele2 = new HashMap<Allele, Allele>();
Map<Allele, Allele> allele2ToAllele1 = new HashMap<Allele, Allele>();
// Note the segregation of the alleles for the reference genome:
allele1ToAllele2.put(vc1.getReference(), vc2.getReference());
allele2ToAllele1.put(vc2.getReference(), vc1.getReference());
// Note the segregation of the alleles for each sample (and check that it is consistent with the
// reference and all previous samples).
for (final Genotype gt1 : vc1.getGenotypes()) {
Genotype gt2 = vc2.getGenotype(gt1.getSampleName());
List<Allele> site1Alleles = gt1.getAlleles();
List<Allele> site2Alleles = gt2.getAlleles();
Iterator<Allele> all2It = site2Alleles.iterator();
for (Allele all1 : site1Alleles) {
Allele all2 = all2It.next();
Allele all1To2 = allele1ToAllele2.get(all1);
if (all1To2 == null) allele1ToAllele2.put(all1, all2);
else if (!all1To2.equals(all2)) // all1 segregates with two different alleles at site 2
return false;
Allele all2To1 = allele2ToAllele1.get(all2);
if (all2To1 == null) allele2ToAllele1.put(all2, all1);
else if (!all2To1.equals(all1)) // all2 segregates with two different alleles at site 1
return false;
}
}
return true;
}
private static Allele determineReferenceAllele(List<VariantContext> VCs) {
Allele ref = null;
for (VariantContext vc : VCs) {
Allele myRef = vc.getReference();
if (ref == null || ref.length() < myRef.length()) ref = myRef;
else if (ref.length() == myRef.length() && !ref.equals(myRef))
throw new UserException.BadInput(
String.format(
"The provided variant file(s) have inconsistent references for the same position(s) at %s:%d, %s vs. %s",
vc.getChr(), vc.getStart(), ref, myRef));
}
return ref;
}
private static final boolean hasPLIncompatibleAlleles(
final Collection<Allele> alleleSet1, final Collection<Allele> alleleSet2) {
final Iterator<Allele> it1 = alleleSet1.iterator();
final Iterator<Allele> it2 = alleleSet2.iterator();
while (it1.hasNext() && it2.hasNext()) {
final Allele a1 = it1.next();
final Allele a2 = it2.next();
if (!a1.equals(a2)) return true;
}
// by this point, at least one of the iterators is empty. All of the elements
// we've compared are equal up until this point. But it's possible that the
// sets aren't the same size, which is indicated by the test below. If they
// are of the same size, though, the sets are compatible
return it1.hasNext() || it2.hasNext();
}