private byte[] generateHaplotype(
final List<VariantContext> sourceVCs, final ReferenceContext refContext) {
final StringBuilder sb = new StringBuilder();
final int startPos = refContext.getWindow().getStart();
int currentPos = startPos;
final byte[] reference = refContext.getBases();
for (final VariantContext vc : sourceVCs) {
// add any missing reference context
int vcStart = vc.getStart();
final int refAlleleLength = vc.getReference().length();
if (refAlleleLength
== vc.getEnd()
- vc.getStart()) // this is a deletion (whereas for other events the padding base
// isn't part of the position)
vcStart++;
while (currentPos < vcStart) sb.append((char) reference[currentPos++ - startPos]);
// add the alt allele
sb.append(vc.getAlternateAllele(0).getBaseString());
// skip the reference allele
currentPos += refAlleleLength;
}
// add any missing reference context
final int stopPos = refContext.getWindow().getStop();
while (currentPos < stopPos) sb.append((char) reference[currentPos++ - startPos]);
return sb.toString().getBytes();
}
private void resolveByHaplotype(final ReferenceContext refContext) {
final byte[] source1Haplotype = generateHaplotype(sourceVCs1, refContext);
final byte[] source2Haplotype = generateHaplotype(sourceVCs2, refContext);
final SWPairwiseAlignment swConsensus1 =
new SWPairwiseAlignment(
refContext.getBases(), source1Haplotype, SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND);
final SWPairwiseAlignment swConsensus2 =
new SWPairwiseAlignment(
refContext.getBases(), source2Haplotype, SW_MATCH, SW_MISMATCH, SW_GAP, SW_GAP_EXTEND);
// protect against SW failures
if (swConsensus1.getCigar().toString().contains("S")
|| swConsensus1.getCigar().getReferenceLength() < 20
|| swConsensus2.getCigar().toString().contains("S")
|| swConsensus2.getCigar().getReferenceLength() < 20) {
// TODO -- handle errors appropriately
logger.debug("Bad SW alignment; aborting at " + refContext.getLocus());
return;
}
// order results by start position
final TreeMap<Integer, VariantContext> source1Map =
new TreeMap<Integer, VariantContext>(
HaplotypeCallerGenotypingEngine.generateVCsFromAlignment(
new Haplotype(source1Haplotype, false, 0, swConsensus1.getCigar()),
refContext.getBases(),
refContext.getWindow(),
source1));
final TreeMap<Integer, VariantContext> source2Map =
new TreeMap<Integer, VariantContext>(
HaplotypeCallerGenotypingEngine.generateVCsFromAlignment(
new Haplotype(source2Haplotype, false, 0, swConsensus2.getCigar()),
refContext.getBases(),
refContext.getWindow(),
source2));
if (source1Map.size() == 0 || source2Map.size() == 0) {
// TODO -- handle errors appropriately
logger.debug("No source alleles; aborting at " + refContext.getLocus());
return;
}
// create lists and test for equality
final List<VariantContext> source1Alleles = new ArrayList<VariantContext>(source1Map.values());
final List<VariantContext> source2Alleles = new ArrayList<VariantContext>(source2Map.values());
writeAndPurgeAllEqualVariants(source1Alleles, source2Alleles, SAME_BY_HAPLOTYPE_STATUS);
if (source1Alleles.isEmpty()) {
writeAll(source2Alleles, source2, null);
} else if (source2Alleles.isEmpty()) {
writeAll(source1Alleles, source1, null);
} else {
writeDifferences(source1Alleles, source2Alleles);
}
}
private Collection<VariantContext> getVariantContexts(
RefMetaDataTracker tracker, ReferenceContext ref) {
List<Feature> features = tracker.getValues(variants, ref.getLocus());
List<VariantContext> VCs = new ArrayList<VariantContext>(features.size());
for (Feature record : features) {
if (VariantContextAdaptors.canBeConvertedToVariantContext(record)) {
// we need to special case the HapMap format because indels aren't handled correctly
if (record instanceof RawHapMapFeature) {
// is it an indel?
RawHapMapFeature hapmap = (RawHapMapFeature) record;
if (hapmap.getAlleles()[0].equals(RawHapMapFeature.NULL_ALLELE_STRING)
|| hapmap.getAlleles()[1].equals(RawHapMapFeature.NULL_ALLELE_STRING)) {
// get the dbsnp object corresponding to this record (needed to help us distinguish
// between insertions and deletions)
VariantContext dbsnpVC = getDbsnp(hapmap.getName());
if (dbsnpVC == null || dbsnpVC.isMixed()) continue;
Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
alleleMap.put(
RawHapMapFeature.DELETION,
Allele.create(ref.getBase(), dbsnpVC.isSimpleInsertion()));
alleleMap.put(
RawHapMapFeature.INSERTION,
Allele.create(
(char) ref.getBase() + ((RawHapMapFeature) record).getAlleles()[1],
!dbsnpVC.isSimpleInsertion()));
hapmap.setActualAlleles(alleleMap);
// also, use the correct positioning for insertions
hapmap.updatePosition(dbsnpVC.getStart());
if (hapmap.getStart() < ref.getWindow().getStart()) {
logger.warn(
"Hapmap record at "
+ ref.getLocus()
+ " represents an indel too large to be converted; skipping...");
continue;
}
}
}
// ok, we might actually be able to turn this record in a variant context
VariantContext vc =
VariantContextAdaptors.toVariantContext(variants.getName(), record, ref);
if (vc != null) // sometimes the track has odd stuff in it that can't be converted
VCs.add(vc);
}
}
return VCs;
}
