/** * Returns the GenotypesLikelihoods data associated with this Genotype, or null if missing * @return null or a GenotypesLikelihood object for this sample's PL field */ public GenotypeLikelihoods getLikelihoods() { return hasLikelihoods() ? GenotypeLikelihoods.fromPLs(getPL()) : null; }
/** * Returns the GenotypesLikelihoods data associated with this Genotype, or null if missing * @return null or a GenotypesLikelihood object for this sample's PL field */ public GenotypeLikelihoods getLikelihoods() { return hasLikelihoods() ? GenotypeLikelihoods.fromPLs(getPL()) : null; }
/** * Returns the GenotypesLikelihoods data associated with this Genotype, or null if missing * @return null or a GenotypesLikelihood object for this sample's PL field */ @Ensures("(hasLikelihoods() && result != null) || (! hasLikelihoods() && result == null)") public GenotypeLikelihoods getLikelihoods() { return hasLikelihoods() ? GenotypeLikelihoods.fromPLs(getPL()) : null; }
newLog10GQ = GenotypeLikelihoods.getGQLog10FromLikelihoods(indexOfMostLikely, GenotypeLikelihoods.fromPLs(newPLs).getAsVector()); } else { newPLs = null;
newLog10GQ = GenotypeLikelihoods.getGQLog10FromLikelihoods(indexOfMostLikely, GenotypeLikelihoods.fromPLs(newPLs).getAsVector()); } else { newPLs = null;
newPLs[i] = Math.min(maximalPLDifference, pls[i]); hFp.addToLogLikelihoods(snp, usableSnp.getAlleles(), GenotypeLikelihoods.fromPLs(newPLs).getAsVector()); fp.add(hFp); } else {
newPLs[i] = Math.min(maximalPLDifference, pls[i]); hFp.addToLogLikelihoods(snp, usableSnp.getAlleles(), GenotypeLikelihoods.fromPLs(newPLs).getAsVector()); fp.add(hFp); } else {