private void writeSampleLikelihoods( StringBuffer out, VariantContext vc, double[] log10Likelihoods) { if (VQSRCalibrator != null) { log10Likelihoods = VQSRCalibrator.includeErrorRateInLikelihoods(VQSLOD_KEY, vc, log10Likelihoods); } double[] normalizedLikelihoods = MathUtils.normalizeFromLog10(log10Likelihoods); // see if we need to randomly mask out genotype in this position. for (double likeVal : normalizedLikelihoods) { out.append(formatter.format(likeVal)); // out.append(String.format("%5.4f ",likeVal)); } }
public void writeBeagleOutput( VariantContext preferredVC, VariantContext otherVC, boolean isValidationSite, double prior) { GenomeLoc currentLoc = VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), preferredVC); StringBuffer beagleOut = new StringBuffer(); String marker = String.format("%s:%d ", currentLoc.getContig(), currentLoc.getStart()); beagleOut.append(marker); if (markers != null) markers.append(marker).append("\t").append(Integer.toString(markerCounter++)).append("\t"); for (Allele allele : preferredVC.getAlleles()) { String bglPrintString; if (allele.isNoCall() || allele.isNull()) bglPrintString = "-"; else bglPrintString = allele.getBaseString(); // get rid of * in case of reference allele beagleOut.append(String.format("%s ", bglPrintString)); if (markers != null) markers.append(bglPrintString).append("\t"); } if (markers != null) markers.append("\n"); GenotypesContext preferredGenotypes = preferredVC.getGenotypes(); GenotypesContext otherGenotypes = goodSite(otherVC) ? otherVC.getGenotypes() : null; for (String sample : samples) { boolean isMaleOnChrX = CHECK_IS_MALE_ON_CHR_X && getSample(sample).getGender() == Gender.MALE; Genotype genotype; boolean isValidation; // use sample as key into genotypes structure if (preferredGenotypes.containsSample(sample)) { genotype = preferredGenotypes.get(sample); isValidation = isValidationSite; } else if (otherGenotypes != null && otherGenotypes.containsSample(sample)) { genotype = otherGenotypes.get(sample); isValidation = !isValidationSite; } else { // there is magically no genotype for this sample. throw new StingException( "Sample " + sample + " arose with no genotype in variant or validation VCF. This should never happen."); } /* * Use likelihoods if: is validation, prior is negative; or: is not validation, has genotype key */ double[] log10Likelihoods = null; if ((isValidation && prior < 0.0) || genotype.hasLikelihoods()) { log10Likelihoods = genotype.getLikelihoods().getAsVector(); // see if we need to randomly mask out genotype in this position. if (GenomeAnalysisEngine.getRandomGenerator().nextDouble() <= insertedNoCallRate) { // we are masking out this genotype log10Likelihoods = isMaleOnChrX ? HAPLOID_FLAT_LOG10_LIKELIHOODS : DIPLOID_FLAT_LOG10_LIKELIHOODS; } if (isMaleOnChrX) { log10Likelihoods[1] = -255; // todo -- warning this is dangerous for multi-allele case } } /** otherwise, use the prior uniformly */ else if (!isValidation && genotype.isCalled() && !genotype.hasLikelihoods()) { // hack to deal with input VCFs with no genotype likelihoods. Just assume the called // genotype // is confident. This is useful for Hapmap and 1KG release VCFs. double AA = (1.0 - prior) / 2.0; double AB = (1.0 - prior) / 2.0; double BB = (1.0 - prior) / 2.0; if (genotype.isHomRef()) { AA = prior; } else if (genotype.isHet()) { AB = prior; } else if (genotype.isHomVar()) { BB = prior; } log10Likelihoods = MathUtils.toLog10(new double[] {AA, isMaleOnChrX ? 0.0 : AB, BB}); } else { log10Likelihoods = isMaleOnChrX ? HAPLOID_FLAT_LOG10_LIKELIHOODS : DIPLOID_FLAT_LOG10_LIKELIHOODS; } writeSampleLikelihoods(beagleOut, preferredVC, log10Likelihoods); } beagleWriter.println(beagleOut.toString()); }