/** * Helper function to add the read underneath a pileup element to the map * * @param p Pileup element * @param a Corresponding allele * @param likelihood Allele likelihood */ public void add(PileupElement p, Allele a, Double likelihood) { if (p == null) throw new IllegalArgumentException("Pileup element cannot be null"); if (p.getRead() == null) throw new IllegalArgumentException("Read underlying pileup element cannot be null"); if (a == null) throw new IllegalArgumentException("Allele for add() cannot be null"); add(p.getRead(), a, likelihood); }
public Event map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { boolean hasIndel = false; boolean hasInsertion = false; boolean hasPointEvent = false; int furthestStopPos = -1; // look at the rods for indels or SNPs if (tracker != null) { for (VariantContext vc : tracker.getValues(known)) { switch (vc.getType()) { case INDEL: hasIndel = true; if (vc.isSimpleInsertion()) hasInsertion = true; break; case SNP: hasPointEvent = true; break; case MIXED: hasPointEvent = true; hasIndel = true; if (vc.isSimpleInsertion()) hasInsertion = true; break; default: break; } if (hasIndel) furthestStopPos = vc.getEnd(); } } // look at the normal context to get deletions and positions with high entropy final ReadBackedPileup pileup = context.getBasePileup(); int mismatchQualities = 0, totalQualities = 0; final byte refBase = ref.getBase(); for (PileupElement p : pileup) { // check the ends of the reads to see how far they extend furthestStopPos = Math.max(furthestStopPos, p.getRead().getAlignmentEnd()); // is it a deletion or insertion? if (p.isDeletion() || p.isBeforeInsertion()) { hasIndel = true; if (p.isBeforeInsertion()) hasInsertion = true; } // look for mismatches else if (lookForMismatchEntropy) { if (p.getBase() != refBase) mismatchQualities += p.getQual(); totalQualities += p.getQual(); } } // make sure we're supposed to look for high entropy if (lookForMismatchEntropy && pileup.getNumberOfElements() >= minReadsAtLocus && (double) mismatchQualities / (double) totalQualities >= mismatchThreshold) hasPointEvent = true; // return null if no event occurred if (!hasIndel && !hasPointEvent) return null; // return null if we didn't find any usable reads/rods associated with the event if (furthestStopPos == -1) return null; GenomeLoc eventLoc = context.getLocation(); if (hasInsertion) eventLoc = getToolkit() .getGenomeLocParser() .createGenomeLoc(eventLoc.getContig(), eventLoc.getStart(), eventLoc.getStart() + 1); EVENT_TYPE eventType = (hasIndel ? (hasPointEvent ? EVENT_TYPE.BOTH : EVENT_TYPE.INDEL_EVENT) : EVENT_TYPE.POINT_EVENT); return new Event(eventLoc, furthestStopPos, eventType); }
@Override protected boolean isUsableBase(final PileupElement p) { return super.isUsableBase(p) && p.getRead().getCigar() != null; }
@Override protected Double getElementForPileupElement(final PileupElement p) { final int offset = AlignmentUtils.calcAlignmentByteArrayOffset(p.getRead().getCigar(), p, 0, 0); return (double) AnnotationUtils.getFinalVariantReadPosition(p.getRead(), offset); }
public Map<Allele, Double> getLikelihoodsAssociatedWithPileupElement(final PileupElement p) { if (!likelihoodReadMap.containsKey(p.getRead())) return null; return likelihoodReadMap.get(p.getRead()); }
/** * Does the current map contain the key associated with a particular SAM record in pileup? * * @param p Pileup element * @return true if the map contains pileup element, else false */ public boolean containsPileupElement(final PileupElement p) { return likelihoodReadMap.containsKey(p.getRead()); }