private static Type typeOfBiallelicVariant(Allele ref, Allele allele) {
if (ref.isSymbolic())
throw new IllegalStateException(
"Unexpected error: encountered a record with a symbolic reference allele");
if (allele.isSymbolic()) return Type.SYMBOLIC;
if (ref.length() == allele.length()) {
if (allele.length() == 1) return Type.SNP;
else return Type.MNP;
}
// Important note: previously we were checking that one allele is the prefix of the other.
// However, that's not an
// appropriate check as can be seen from the following example:
// REF = CTTA and ALT = C,CT,CA
// This should be assigned the INDEL type but was being marked as a MIXED type because of the
// prefix check.
// In truth, it should be absolutely impossible to return a MIXED type from this method because
// it simply
// performs a pairwise comparison of a single alternate allele against the reference allele
// (whereas the MIXED type
// is reserved for cases of multiple alternate alleles of different types). Therefore, if we've
// reached this point
// in the code (so we're not a SNP, MNP, or symbolic allele), we absolutely must be an INDEL.
return Type.INDEL;
// old incorrect logic:
// if (oneIsPrefixOfOther(ref, allele))
// return Type.INDEL;
// else
// return Type.MIXED;
}
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 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);
}
}
/**
* Gets the sizes of the alternate alleles if they are insertion/deletion events, and returns a
* list of their sizes
*
* @return a list of indel lengths ( null if not of type indel or mixed )
*/
public List<Integer> getIndelLengths() {
if (getType() != Type.INDEL && getType() != Type.MIXED) {
return null;
}
List<Integer> lengths = new ArrayList<Integer>();
for (Allele a : getAlternateAlleles()) {
lengths.add(a.length() - getReference().length());
}
return lengths;
}
private RepeatDetectorTest(
boolean isTrueRepeat, String ref, String refAlleleString, String... altAlleleStrings) {
super(RepeatDetectorTest.class);
this.ref = "N" + ref; // add a dummy base for the event here
this.isTrueRepeat = isTrueRepeat;
List<Allele> alleles = new LinkedList<Allele>();
final Allele refAllele = Allele.create(refAlleleString, true);
alleles.add(refAllele);
for (final String altString : altAlleleStrings) {
final Allele alt = Allele.create(altString, false);
alleles.add(alt);
}
VariantContextBuilder builder =
new VariantContextBuilder("test", "chr1", 1, 1 + refAllele.length(), alleles);
this.vc = builder.make();
}
public static VariantContext createVariantContextWithTrimmedAlleles(VariantContext inputVC) {
// see if we need to trim common reference base from all alleles
boolean trimVC;
// We need to trim common reference base from all alleles in all genotypes if a ref base is
// common to all alleles
Allele refAllele = inputVC.getReference();
if (!inputVC.isVariant()) trimVC = false;
else if (refAllele.isNull()) trimVC = false;
else {
trimVC =
(AbstractVCFCodec.computeForwardClipping(
new ArrayList<Allele>(inputVC.getAlternateAlleles()),
inputVC.getReference().getDisplayString())
> 0);
}
// nothing to do if we don't need to trim bases
if (trimVC) {
List<Allele> alleles = new ArrayList<Allele>();
GenotypesContext genotypes = GenotypesContext.create();
// set the reference base for indels in the attributes
Map<String, Object> attributes = new TreeMap<String, Object>(inputVC.getAttributes());
Map<Allele, Allele> originalToTrimmedAlleleMap = new HashMap<Allele, Allele>();
for (Allele a : inputVC.getAlleles()) {
if (a.isSymbolic()) {
alleles.add(a);
originalToTrimmedAlleleMap.put(a, a);
} else {
// get bases for current allele and create a new one with trimmed bases
byte[] newBases = Arrays.copyOfRange(a.getBases(), 1, a.length());
Allele trimmedAllele = Allele.create(newBases, a.isReference());
alleles.add(trimmedAllele);
originalToTrimmedAlleleMap.put(a, trimmedAllele);
}
}
// detect case where we're trimming bases but resulting vc doesn't have any null allele. In
// that case, we keep original representation
// example: mixed records such as {TA*,TGA,TG}
boolean hasNullAlleles = false;
for (Allele a : originalToTrimmedAlleleMap.values()) {
if (a.isNull()) hasNullAlleles = true;
if (a.isReference()) refAllele = a;
}
if (!hasNullAlleles) return inputVC;
// now we can recreate new genotypes with trimmed alleles
for (final Genotype genotype : inputVC.getGenotypes()) {
List<Allele> originalAlleles = genotype.getAlleles();
List<Allele> trimmedAlleles = new ArrayList<Allele>();
for (Allele a : originalAlleles) {
if (a.isCalled()) trimmedAlleles.add(originalToTrimmedAlleleMap.get(a));
else trimmedAlleles.add(Allele.NO_CALL);
}
genotypes.add(Genotype.modifyAlleles(genotype, trimmedAlleles));
}
final VariantContextBuilder builder = new VariantContextBuilder(inputVC);
return builder
.alleles(alleles)
.genotypes(genotypes)
.attributes(attributes)
.referenceBaseForIndel(new Byte(inputVC.getReference().getBases()[0]))
.make();
}
return inputVC;
}