protected final void printCallInfo(
final VariantContext vc,
final double[] log10AlleleFrequencyPriors,
final long runtimeNano,
final AFCalcResult result) {
printCallElement(vc, "type", "ignore", vc.getType());
int allelei = 0;
for (final Allele a : vc.getAlleles())
printCallElement(vc, "allele", allelei++, a.getDisplayString());
for (final Genotype g : vc.getGenotypes())
printCallElement(vc, "PL", g.getSampleName(), g.getLikelihoodsString());
for (int priorI = 0; priorI < log10AlleleFrequencyPriors.length; priorI++)
printCallElement(vc, "priorI", priorI, log10AlleleFrequencyPriors[priorI]);
printCallElement(vc, "runtime.nano", "ignore", runtimeNano);
printCallElement(vc, "log10PosteriorOfAFEq0", "ignore", result.getLog10PosteriorOfAFEq0());
printCallElement(vc, "log10PosteriorOfAFGt0", "ignore", result.getLog10PosteriorOfAFGT0());
for (final Allele allele : result.getAllelesUsedInGenotyping()) {
if (allele.isNonReference()) {
printCallElement(vc, "MLE", allele, result.getAlleleCountAtMLE(allele));
printCallElement(
vc, "pNonRefByAllele", allele, result.getLog10PosteriorOfAFGt0ForAllele(allele));
}
}
callReport.flush();
}
/**
* Read in a list of ExactCall objects from reader, keeping only those with starts in startsToKeep
* or all sites (if this is empty)
*
* @param reader a just-opened reader sitting at the start of the file
* @param startsToKeep a list of start position of the calls to keep, or empty if all calls should
* be kept
* @param parser a genome loc parser to create genome locs
* @return a list of ExactCall objects in reader
* @throws IOException
*/
public static List<ExactCall> readExactLog(
final BufferedReader reader, final List<Integer> startsToKeep, GenomeLocParser parser)
throws IOException {
if (reader == null) throw new IllegalArgumentException("reader cannot be null");
if (startsToKeep == null) throw new IllegalArgumentException("startsToKeep cannot be null");
if (parser == null) throw new IllegalArgumentException("GenomeLocParser cannot be null");
List<ExactCall> calls = new LinkedList<ExactCall>();
// skip the header line
reader.readLine();
// skip the first "type" line
reader.readLine();
while (true) {
final VariantContextBuilder builder = new VariantContextBuilder();
final List<Allele> alleles = new ArrayList<Allele>();
final List<Genotype> genotypes = new ArrayList<Genotype>();
final double[] posteriors = new double[2];
final double[] priors = MathUtils.normalizeFromLog10(new double[] {0.5, 0.5}, true);
final List<Integer> mle = new ArrayList<Integer>();
final Map<Allele, Double> log10pNonRefByAllele = new HashMap<Allele, Double>();
long runtimeNano = -1;
GenomeLoc currentLoc = null;
while (true) {
final String line = reader.readLine();
if (line == null) return calls;
final String[] parts = line.split("\t");
final GenomeLoc lineLoc = parser.parseGenomeLoc(parts[0]);
final String variable = parts[1];
final String key = parts[2];
final String value = parts[3];
if (currentLoc == null) currentLoc = lineLoc;
if (variable.equals("type")) {
if (startsToKeep.isEmpty() || startsToKeep.contains(currentLoc.getStart())) {
builder.alleles(alleles);
final int stop = currentLoc.getStart() + alleles.get(0).length() - 1;
builder.chr(currentLoc.getContig()).start(currentLoc.getStart()).stop(stop);
builder.genotypes(genotypes);
final int[] mleInts = ArrayUtils.toPrimitive(mle.toArray(new Integer[] {}));
final AFCalcResult result =
new AFCalcResult(mleInts, 1, alleles, posteriors, priors, log10pNonRefByAllele);
calls.add(new ExactCall(builder.make(), runtimeNano, result));
}
break;
} else if (variable.equals("allele")) {
final boolean isRef = key.equals("0");
alleles.add(Allele.create(value, isRef));
} else if (variable.equals("PL")) {
final GenotypeBuilder gb = new GenotypeBuilder(key);
gb.PL(GenotypeLikelihoods.fromPLField(value).getAsPLs());
genotypes.add(gb.make());
} else if (variable.equals("log10PosteriorOfAFEq0")) {
posteriors[0] = Double.valueOf(value);
} else if (variable.equals("log10PosteriorOfAFGt0")) {
posteriors[1] = Double.valueOf(value);
} else if (variable.equals("MLE")) {
mle.add(Integer.valueOf(value));
} else if (variable.equals("pNonRefByAllele")) {
final Allele a = Allele.create(key);
log10pNonRefByAllele.put(a, Double.valueOf(value));
} else if (variable.equals("runtime.nano")) {
runtimeNano = Long.valueOf(value);
} else {
// nothing to do
}
}
}
}