public static VariantContext getVCFromAllelesRod(
RefMetaDataTracker tracker,
ReferenceContext ref,
GenomeLoc loc,
boolean requireSNP,
Logger logger,
final RodBinding<VariantContext> allelesBinding) {
if (tracker == null || ref == null || logger == null) return null;
VariantContext vc = null;
// search for usable record
for (final VariantContext vc_input : tracker.getValues(allelesBinding, loc)) {
if (vc_input != null && !vc_input.isFiltered() && (!requireSNP || vc_input.isSNP())) {
if (vc == null) {
vc = vc_input;
} else {
logger.warn(
"Multiple valid VCF records detected in the alleles input file at site "
+ ref.getLocus()
+ ", only considering the first record");
}
}
}
return vc;
}
public static BaseUtils.BaseSubstitutionType getSNPSubstitutionType(VariantContext context) {
if (!context.isSNP() || !context.isBiallelic())
throw new IllegalStateException(
"Requested SNP substitution type for bialleic non-SNP " + context);
return BaseUtils.SNPSubstitutionType(
context.getReference().getBases()[0], context.getAlternateAllele(0).getBases()[0]);
}
public Map<String, Object> annotate(
final RefMetaDataTracker tracker,
final AnnotatorCompatible walker,
final ReferenceContext ref,
final Map<String, AlignmentContext> stratifiedContexts,
final VariantContext vc,
final Map<String, PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
int run;
if (vc.isMixed()) {
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%s", "MIXED"));
return map;
} else if (vc.isIndel()) {
String type = "";
if (!vc.isBiallelic()) type = "MULTIALLELIC_INDEL";
else {
if (vc.isSimpleInsertion()) type = "INS.";
else if (vc.isSimpleDeletion()) type = "DEL.";
else type = "OTHER.";
ArrayList<Integer> inds = IndelUtils.findEventClassificationIndex(vc, ref);
for (int k : inds) {
type = type + IndelUtils.getIndelClassificationName(k) + ".";
}
}
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%s", type));
return map;
} else {
return null;
}
}
@Test(dataProvider = "mergeAlleles")
public void testMergeAlleles(MergeAllelesTest cfg) {
final List<VariantContext> inputs = new ArrayList<VariantContext>();
int i = 0;
for (final List<Allele> alleles : cfg.inputs) {
final String name = "vcf" + ++i;
inputs.add(makeVC(name, alleles));
}
final List<String> priority = vcs2priority(inputs);
final VariantContext merged =
VariantContextUtils.simpleMerge(
genomeLocParser,
inputs,
priority,
VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
VariantContextUtils.GenotypeMergeType.PRIORITIZE,
false,
false,
"set",
false,
false);
Assert.assertEquals(merged.getAlleles(), cfg.expected);
}
/**
* Checks if vc has a variant call for (at least one of) the samples.
*
* @param vc the variant rod VariantContext. Here, the variant is the dataset you're looking for
* discordances to (e.g. HapMap)
* @param compVCs the comparison VariantContext (discordance
* @return
*/
private boolean isDiscordant(VariantContext vc, Collection<VariantContext> compVCs) {
if (vc == null) return false;
// if we're not looking at specific samples then the absence of a compVC means discordance
if (NO_SAMPLES_SPECIFIED) return (compVCs == null || compVCs.isEmpty());
// check if we find it in the variant rod
Map<String, Genotype> genotypes = vc.getGenotypes(samples);
for (Genotype g : genotypes.values()) {
if (sampleHasVariant(g)) {
// There is a variant called (or filtered with not exclude filtered option set) that is not
// HomRef for at least one of the samples.
if (compVCs == null) return true;
// Look for this sample in the all vcs of the comp ROD track.
boolean foundVariant = false;
for (VariantContext compVC : compVCs) {
if (sampleHasVariant(compVC.getGenotype(g.getSampleName()))) {
foundVariant = true;
break;
}
}
// if (at least one sample) was not found in all VCs of the comp ROD, we have discordance
if (!foundVariant) return true;
}
}
return false; // we only get here if all samples have a variant in the comp rod.
}
private boolean isConcordant(VariantContext vc, Collection<VariantContext> compVCs) {
if (vc == null || compVCs == null || compVCs.isEmpty()) return false;
// if we're not looking for specific samples then the fact that we have both VCs is enough to
// call it concordant.
if (NO_SAMPLES_SPECIFIED) return true;
// make a list of all samples contained in this variant VC that are being tracked by the user
// command line arguments.
Set<String> variantSamples = vc.getSampleNames();
variantSamples.retainAll(samples);
// check if we can find all samples from the variant rod in the comp rod.
for (String sample : variantSamples) {
boolean foundSample = false;
for (VariantContext compVC : compVCs) {
Genotype varG = vc.getGenotype(sample);
Genotype compG = compVC.getGenotype(sample);
if (haveSameGenotypes(varG, compG)) {
foundSample = true;
break;
}
}
// if at least one sample doesn't have the same genotype, we don't have concordance
if (!foundSample) {
return false;
}
}
return true;
}
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();
}
@Override
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
// First, verify that the metadata tracker is not null (meaning there is a variant at this locus
// to process).
if (tracker != null) {
// Get all of the "VariantContext" objects that span this locus. A VariantContext represents
// a line in a VCF file.
Collection<VariantContext> vcs =
tracker.getVariantContexts(ref, "variant", null, context.getLocation(), true, false);
// There may be more than one variant at this locus. Process them all.
for (VariantContext vc : vcs) {
out.println(
"Hello, ref="
+ vc.getReference()
+ ",alt="
+ vc.getAltAlleleWithHighestAlleleCount()
+ " at "
+ vc.getChr()
+ ":"
+ vc.getStart());
}
// Return 1, indicating that we saw a variant.
return 1;
}
// We saw nothing of interest, so return 0.
return 0;
}
@Test
public void testAnnotationSet() {
for (final boolean annotate : Arrays.asList(true, false)) {
for (final String set : Arrays.asList("set", "combine", "x")) {
final List<String> priority = Arrays.asList("1", "2");
VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS);
VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS);
final VariantContext merged =
VariantContextUtils.simpleMerge(
genomeLocParser,
Arrays.asList(vc1, vc2),
priority,
VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
VariantContextUtils.GenotypeMergeType.PRIORITIZE,
annotate,
false,
set,
false,
false);
if (annotate)
Assert.assertEquals(merged.getAttribute(set), VariantContextUtils.MERGE_INTERSECTION);
else Assert.assertFalse(merged.hasAttribute(set));
}
}
}
@Test(dataProvider = "mergeFiltered")
public void testMergeFiltered(MergeFilteredTest cfg) {
final List<String> priority = vcs2priority(cfg.inputs);
final VariantContext merged =
VariantContextUtils.simpleMerge(
genomeLocParser,
cfg.inputs,
priority,
cfg.type,
VariantContextUtils.GenotypeMergeType.PRIORITIZE,
true,
false,
"set",
false,
false);
// test alleles are equal
Assert.assertEquals(merged.getAlleles(), cfg.expected.getAlleles());
// test set field
Assert.assertEquals(merged.getAttribute("set"), cfg.setExpected);
// test filter field
Assert.assertEquals(merged.getFilters(), cfg.expected.getFilters());
}
/**
* Returns a context identical to this with the REF and ALT alleles reverse complemented.
*
* @param vc variant context
* @return new vc
*/
public static VariantContext reverseComplement(VariantContext vc) {
// create a mapping from original allele to reverse complemented allele
HashMap<Allele, Allele> alleleMap = new HashMap<Allele, Allele>(vc.getAlleles().size());
for (Allele originalAllele : vc.getAlleles()) {
Allele newAllele;
if (originalAllele.isNoCall() || originalAllele.isNull()) newAllele = originalAllele;
else
newAllele =
Allele.create(
BaseUtils.simpleReverseComplement(originalAllele.getBases()),
originalAllele.isReference());
alleleMap.put(originalAllele, newAllele);
}
// create new Genotype objects
GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples());
for (final Genotype genotype : vc.getGenotypes()) {
List<Allele> newAlleles = new ArrayList<Allele>();
for (Allele allele : genotype.getAlleles()) {
Allele newAllele = alleleMap.get(allele);
if (newAllele == null) newAllele = Allele.NO_CALL;
newAlleles.add(newAllele);
}
newGenotypes.add(Genotype.modifyAlleles(genotype, newAlleles));
}
return new VariantContextBuilder(vc).alleles(alleleMap.values()).genotypes(newGenotypes).make();
}
private static void mergeGenotypes(
GenotypesContext mergedGenotypes,
VariantContext oneVC,
AlleleMapper alleleMapping,
boolean uniqifySamples) {
for (Genotype g : oneVC.getGenotypes()) {
String name = mergedSampleName(oneVC.getSource(), g.getSampleName(), uniqifySamples);
if (!mergedGenotypes.containsSample(name)) {
// only add if the name is new
Genotype newG = g;
if (uniqifySamples || alleleMapping.needsRemapping()) {
final List<Allele> alleles =
alleleMapping.needsRemapping() ? alleleMapping.remap(g.getAlleles()) : g.getAlleles();
newG =
new Genotype(
name,
alleles,
g.getLog10PError(),
g.getFilters(),
g.getAttributes(),
g.isPhased());
}
mergedGenotypes.add(newG);
}
}
}
/**
* Update the attributes of the attributes map in the VariantContextBuilder to reflect the proper
* chromosome-based VCF tags based on the current VC produced by builder.make()
*
* @param builder the VariantContextBuilder we are updating
* @param removeStaleValues should we remove stale values from the mapping?
*/
public static void calculateChromosomeCounts(
VariantContextBuilder builder, boolean removeStaleValues) {
final VariantContext vc = builder.make();
final Map<String, Object> attrs =
calculateChromosomeCounts(
vc, new HashMap<String, Object>(vc.getAttributes()), removeStaleValues);
builder.attributes(attrs);
}
private static final List<String> vcs2priority(final Collection<VariantContext> vcs) {
final List<String> priority = new ArrayList<String>();
for (final VariantContext vc : vcs) {
priority.add(vc.getSource());
}
return priority;
}
public MergedAllelesData(byte[] intermediateBases, VariantContext vc1, VariantContext vc2) {
this.mergedAlleles =
new HashMap<
AlleleOneAndTwo, Allele>(); // implemented equals() and hashCode() for AlleleOneAndTwo
this.intermediateBases = intermediateBases;
this.intermediateLength = this.intermediateBases != null ? this.intermediateBases.length : 0;
this.ensureMergedAllele(vc1.getReference(), vc2.getReference(), true);
}
public static boolean allelesAreSubset(VariantContext vc1, VariantContext vc2) {
// if all alleles of vc1 are a contained in alleles of vc2, return true
if (!vc1.getReference().equals(vc2.getReference())) return false;
for (Allele a : vc1.getAlternateAlleles()) {
if (!vc2.getAlternateAlleles().contains(a)) return false;
}
return true;
}
@Override
public String toString() {
return String.format(
"ExactCall %s:%d alleles=%s nSamples=%s orig.pNonRef=%.2f orig.runtime=%s",
vc.getChr(),
vc.getStart(),
vc.getAlleles(),
vc.getNSamples(),
originalCall.getLog10PosteriorOfAFGT0(),
new AutoFormattingTime(runtime / 1e9).toString());
}
private int getIndex(VariantContext vc) {
int i = priorityListOfVCs.indexOf(vc.getSource());
if (i == -1)
throw new UserException.BadArgumentValue(
Utils.join(",", priorityListOfVCs),
"Priority list "
+ priorityListOfVCs
+ " doesn't contain variant context "
+ vc.getSource());
return i;
}
static boolean allSamplesAreMergeable(VariantContext vc1, VariantContext vc2) {
// Check that each sample's genotype in vc2 is uniquely appendable onto its genotype in vc1:
for (final Genotype gt1 : vc1.getGenotypes()) {
Genotype gt2 = vc2.getGenotype(gt1.getSampleName());
if (!alleleSegregationIsKnown(gt1, gt2)) // can merge if: phased, or if either is a hom
return false;
}
return true;
}
@Requires({
"vc != null",
"variable != null",
"key != null",
"value != null",
"callReport != null"
})
private void printCallElement(
final VariantContext vc, final Object variable, final Object key, final Object value) {
final String loc = String.format("%s:%d", vc.getChr(), vc.getStart());
callReport.println(Utils.join("\t", Arrays.asList(loc, variable, key, value)));
}
private static void verifyUniqueSampleNames(Collection<VariantContext> unsortedVCs) {
Set<String> names = new HashSet<String>();
for (VariantContext vc : unsortedVCs) {
for (String name : vc.getSampleNames()) {
// System.out.printf("Checking %s %b%n", name, names.contains(name));
if (names.contains(name))
throw new UserException(
"REQUIRE_UNIQUE sample names is true but duplicate names were discovered " + name);
}
names.addAll(vc.getSampleNames());
}
}
/**
* Update the attributes of the attributes map given the VariantContext to reflect the proper
* chromosome-based VCF tags
*
* @param vc the VariantContext
* @param attributes the attributes map to populate; must not be null; may contain old values
* @param removeStaleValues should we remove stale values from the mapping?
* @return the attributes map provided as input, returned for programming convenience
*/
public static Map<String, Object> calculateChromosomeCounts(
VariantContext vc, Map<String, Object> attributes, boolean removeStaleValues) {
final int AN = vc.getCalledChrCount();
// if everyone is a no-call, remove the old attributes if requested
if (AN == 0 && removeStaleValues) {
if (attributes.containsKey(VCFConstants.ALLELE_COUNT_KEY))
attributes.remove(VCFConstants.ALLELE_COUNT_KEY);
if (attributes.containsKey(VCFConstants.ALLELE_FREQUENCY_KEY))
attributes.remove(VCFConstants.ALLELE_FREQUENCY_KEY);
if (attributes.containsKey(VCFConstants.ALLELE_NUMBER_KEY))
attributes.remove(VCFConstants.ALLELE_NUMBER_KEY);
return attributes;
}
if (vc.hasGenotypes()) {
attributes.put(VCFConstants.ALLELE_NUMBER_KEY, AN);
// if there are alternate alleles, record the relevant tags
if (vc.getAlternateAlleles().size() > 0) {
final ArrayList<String> alleleFreqs = new ArrayList<String>();
final ArrayList<Integer> alleleCounts = new ArrayList<Integer>();
for (Allele allele : vc.getAlternateAlleles()) {
int altChromosomes = vc.getCalledChrCount(allele);
alleleCounts.add(altChromosomes);
if (AN == 0) {
alleleFreqs.add("0.0");
} else {
// todo -- this is a performance problem
final String freq =
String.format(
makePrecisionFormatStringFromDenominatorValue((double) AN),
((double) altChromosomes / (double) AN));
alleleFreqs.add(freq);
}
}
attributes.put(
VCFConstants.ALLELE_COUNT_KEY,
alleleCounts.size() == 1 ? alleleCounts.get(0) : alleleCounts);
attributes.put(
VCFConstants.ALLELE_FREQUENCY_KEY,
alleleFreqs.size() == 1 ? alleleFreqs.get(0) : alleleFreqs);
} else {
attributes.put(VCFConstants.ALLELE_COUNT_KEY, 0);
attributes.put(VCFConstants.ALLELE_FREQUENCY_KEY, 0.0);
}
}
return attributes;
}
private Type getType(VariantContext vc) {
switch (vc.getType()) {
case SNP:
return Type.SNP;
case INDEL:
for (int l : vc.getIndelLengths()) if (Math.abs(l) > MAX_INDEL_LENGTH) return Type.CNV;
return Type.INDEL;
case SYMBOLIC:
return Type.CNV;
default:
// throw new UserException.BadInput("Unexpected variant context type: " + vc);
return null;
}
}
private Map<String, Object> calculateIC(final VariantContext vc) {
final GenotypesContext genotypes =
(founderIds == null || founderIds.isEmpty())
? vc.getGenotypes()
: vc.getGenotypes(founderIds);
if (genotypes == null || genotypes.size() < MIN_SAMPLES) return null;
int idxAA = 0, idxAB = 1, idxBB = 2;
if (!vc.isBiallelic()) {
// for non-bliallelic case, do test with most common alt allele.
// Get then corresponding indeces in GL vectors to retrieve GL of AA,AB and BB.
int[] idxVector = vc.getGLIndecesOfAlternateAllele(vc.getAltAlleleWithHighestAlleleCount());
idxAA = idxVector[0];
idxAB = idxVector[1];
idxBB = idxVector[2];
}
double refCount = 0.0;
double hetCount = 0.0;
double homCount = 0.0;
int N = 0; // number of samples that have likelihoods
for (final Genotype g : genotypes) {
if (g.isNoCall() || !g.hasLikelihoods()) continue;
if (g.getPloidy() != 2) // only work for diploid samples
continue;
N++;
final double[] normalizedLikelihoods =
MathUtils.normalizeFromLog10(g.getLikelihoods().getAsVector());
refCount += normalizedLikelihoods[idxAA];
hetCount += normalizedLikelihoods[idxAB];
homCount += normalizedLikelihoods[idxBB];
}
if (N < MIN_SAMPLES) {
return null;
}
final double p =
(2.0 * refCount + hetCount)
/ (2.0 * (refCount + hetCount + homCount)); // expected reference allele frequency
final double q = 1.0 - p; // expected alternative allele frequency
final double F = 1.0 - (hetCount / (2.0 * p * q * (double) N)); // inbreeding coefficient
Map<String, Object> map = new HashMap<String, Object>();
map.put(getKeyNames().get(0), String.format("%.4f", F));
return map;
}
public Map<String, Object> annotate(
RefMetaDataTracker tracker,
AnnotatorCompatibleWalker walker,
ReferenceContext ref,
AlignmentContext stratifiedContext,
VariantContext vc,
Genotype g) {
if (g == null || !g.isCalled()) return null;
if (vc.isSNP()) return annotateSNP(stratifiedContext, vc);
if (vc.isIndel()) return annotateIndel(stratifiedContext, vc);
return null;
}
public static VariantContext purgeUnallowedGenotypeAttributes(
VariantContext vc, Set<String> allowedAttributes) {
if (allowedAttributes == null) return vc;
GenotypesContext newGenotypes = GenotypesContext.create(vc.getNSamples());
for (final Genotype genotype : vc.getGenotypes()) {
Map<String, Object> attrs = new HashMap<String, Object>();
for (Map.Entry<String, Object> attr : genotype.getAttributes().entrySet()) {
if (allowedAttributes.contains(attr.getKey())) attrs.put(attr.getKey(), attr.getValue());
}
newGenotypes.add(Genotype.modifyAttributes(genotype, attrs));
}
return new VariantContextBuilder(vc).genotypes(newGenotypes).make();
}
private static Allele determineReferenceAllele(List<VariantContext> VCs) {
Allele ref = null;
for (VariantContext vc : VCs) {
Allele myRef = vc.getReference();
if (ref == null || ref.length() < myRef.length()) ref = myRef;
else if (ref.length() == myRef.length() && !ref.equals(myRef))
throw new UserException.BadInput(
String.format(
"The provided variant file(s) have inconsistent references for the same position(s) at %s:%d, %s vs. %s",
vc.getChr(), vc.getStart(), ref, myRef));
}
return ref;
}
/**
* Copy constructor
*
* @param other the VariantContext to copy
*/
protected VariantContext(VariantContext other) {
this(
other.getSource(),
other.getID(),
other.getChr(),
other.getStart(),
other.getEnd(),
other.getAlleles(),
other.getGenotypes(),
other.getLog10PError(),
other.getFiltersMaybeNull(),
other.getAttributes(),
other.REFERENCE_BASE_FOR_INDEL,
NO_VALIDATION);
}
// decide whether we are currently processing SNPs, indels, neither, or both
private List<GenotypeLikelihoodsCalculationModel.Model> getGLModelsToUse(
final RefMetaDataTracker tracker,
final ReferenceContext refContext,
final AlignmentContext rawContext) {
final List<GenotypeLikelihoodsCalculationModel.Model> models =
new ArrayList<GenotypeLikelihoodsCalculationModel.Model>(2);
String modelPrefix = "";
if (UAC.GLmodel.name().toUpperCase().contains("BOTH"))
modelPrefix = UAC.GLmodel.name().toUpperCase().replaceAll("BOTH", "");
if (!UAC.GLmodel.name().contains(GPSTRING)
&& UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY)
modelPrefix = GPSTRING + modelPrefix;
// if we're genotyping given alleles and we have a requested SNP at this position, do SNP
if (UAC.GenotypingMode
== GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES) {
final VariantContext vcInput =
getVCFromAllelesRod(
tracker, refContext, rawContext.getLocation(), false, logger, UAC.alleles);
if (vcInput == null) return models;
if (vcInput.isSNP()) {
// ignore SNPs if the user chose INDEL mode only
if (UAC.GLmodel.name().toUpperCase().contains("BOTH")
|| UAC.GLmodel.name().toUpperCase().contains("SNP"))
models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix + "SNP"));
} else if (vcInput.isIndel() || vcInput.isMixed()) {
// ignore INDELs if the user chose SNP mode only
if (UAC.GLmodel.name().toUpperCase().contains("BOTH")
|| UAC.GLmodel.name().toUpperCase().contains("INDEL"))
models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix + "INDEL"));
}
// No support for other types yet
} else {
if (UAC.GLmodel.name().toUpperCase().contains("BOTH")) {
models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix + "SNP"));
models.add(GenotypeLikelihoodsCalculationModel.Model.valueOf(modelPrefix + "INDEL"));
} else {
models.add(
GenotypeLikelihoodsCalculationModel.Model.valueOf(
modelPrefix + UAC.GLmodel.name().toUpperCase()));
}
}
return models;
}
private static List<String> calcVCFGenotypeKeys(VariantContext vc) {
Set<String> keys = new HashSet<String>();
boolean sawGoodGT = false;
boolean sawGoodQual = false;
boolean sawGenotypeFilter = false;
for (Genotype g : vc.getGenotypes().values()) {
keys.addAll(g.getAttributes().keySet());
if (g.isAvailable()) sawGoodGT = true;
if (g.hasNegLog10PError()) sawGoodQual = true;
if (g.isFiltered() && g.isCalled()) sawGenotypeFilter = true;
}
if (sawGoodQual) keys.add(VCFConstants.GENOTYPE_QUALITY_KEY);
if (sawGenotypeFilter) keys.add(VCFConstants.GENOTYPE_FILTER_KEY);
List<String> sortedList = ParsingUtils.sortList(new ArrayList<String>(keys));
// make sure the GT is first
if (sawGoodGT) {
List<String> newList = new ArrayList<String>(sortedList.size() + 1);
newList.add(VCFConstants.GENOTYPE_KEY);
newList.addAll(sortedList);
sortedList = newList;
}
return sortedList;
}