public static VariantContext createVariantContextWithTrimmedAlleles(VariantContext inputVC) {
// see if we need to trim common reference base from all alleles
boolean trimVC;
// We need to trim common reference base from all alleles in all genotypes if a ref base is
// common to all alleles
Allele refAllele = inputVC.getReference();
if (!inputVC.isVariant()) trimVC = false;
else if (refAllele.isNull()) trimVC = false;
else {
trimVC =
(AbstractVCFCodec.computeForwardClipping(
new ArrayList<Allele>(inputVC.getAlternateAlleles()),
inputVC.getReference().getDisplayString())
> 0);
}
// nothing to do if we don't need to trim bases
if (trimVC) {
List<Allele> alleles = new ArrayList<Allele>();
GenotypesContext genotypes = GenotypesContext.create();
// set the reference base for indels in the attributes
Map<String, Object> attributes = new TreeMap<String, Object>(inputVC.getAttributes());
Map<Allele, Allele> originalToTrimmedAlleleMap = new HashMap<Allele, Allele>();
for (Allele a : inputVC.getAlleles()) {
if (a.isSymbolic()) {
alleles.add(a);
originalToTrimmedAlleleMap.put(a, a);
} else {
// get bases for current allele and create a new one with trimmed bases
byte[] newBases = Arrays.copyOfRange(a.getBases(), 1, a.length());
Allele trimmedAllele = Allele.create(newBases, a.isReference());
alleles.add(trimmedAllele);
originalToTrimmedAlleleMap.put(a, trimmedAllele);
}
}
// detect case where we're trimming bases but resulting vc doesn't have any null allele. In
// that case, we keep original representation
// example: mixed records such as {TA*,TGA,TG}
boolean hasNullAlleles = false;
for (Allele a : originalToTrimmedAlleleMap.values()) {
if (a.isNull()) hasNullAlleles = true;
if (a.isReference()) refAllele = a;
}
if (!hasNullAlleles) return inputVC;
// now we can recreate new genotypes with trimmed alleles
for (final Genotype genotype : inputVC.getGenotypes()) {
List<Allele> originalAlleles = genotype.getAlleles();
List<Allele> trimmedAlleles = new ArrayList<Allele>();
for (Allele a : originalAlleles) {
if (a.isCalled()) trimmedAlleles.add(originalToTrimmedAlleleMap.get(a));
else trimmedAlleles.add(Allele.NO_CALL);
}
genotypes.add(Genotype.modifyAlleles(genotype, trimmedAlleles));
}
final VariantContextBuilder builder = new VariantContextBuilder(inputVC);
return builder
.alleles(alleles)
.genotypes(genotypes)
.attributes(attributes)
.referenceBaseForIndel(new Byte(inputVC.getReference().getBases()[0]))
.make();
}
return inputVC;
}
/**
* 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
}
}
}
}
/**
* Merges VariantContexts into a single hybrid. Takes genotypes for common samples in priority
* order, if provided. If uniqifySamples is true, the priority order is ignored and names are
* created by concatenating the VC name with the sample name
*
* @param genomeLocParser loc parser
* @param unsortedVCs collection of unsorted VCs
* @param priorityListOfVCs priority list detailing the order in which we should grab the VCs
* @param filteredRecordMergeType merge type for filtered records
* @param genotypeMergeOptions merge option for genotypes
* @param annotateOrigin should we annotate the set it came from?
* @param printMessages should we print messages?
* @param setKey the key name of the set
* @param filteredAreUncalled are filtered records uncalled?
* @param mergeInfoWithMaxAC should we merge in info from the VC with maximum allele count?
* @return new VariantContext representing the merge of unsortedVCs
*/
public static VariantContext simpleMerge(
final GenomeLocParser genomeLocParser,
final Collection<VariantContext> unsortedVCs,
final List<String> priorityListOfVCs,
final FilteredRecordMergeType filteredRecordMergeType,
final GenotypeMergeType genotypeMergeOptions,
final boolean annotateOrigin,
final boolean printMessages,
final String setKey,
final boolean filteredAreUncalled,
final boolean mergeInfoWithMaxAC) {
if (unsortedVCs == null || unsortedVCs.size() == 0) return null;
if (annotateOrigin && priorityListOfVCs == null)
throw new IllegalArgumentException(
"Cannot merge calls and annotate their origins without a complete priority list of VariantContexts");
if (genotypeMergeOptions == GenotypeMergeType.REQUIRE_UNIQUE)
verifyUniqueSampleNames(unsortedVCs);
List<VariantContext> prepaddedVCs =
sortVariantContextsByPriority(unsortedVCs, priorityListOfVCs, genotypeMergeOptions);
// Make sure all variant contexts are padded with reference base in case of indels if necessary
List<VariantContext> VCs = new ArrayList<VariantContext>();
for (VariantContext vc : prepaddedVCs) {
// also a reasonable place to remove filtered calls, if needed
if (!filteredAreUncalled || vc.isNotFiltered())
VCs.add(createVariantContextWithPaddedAlleles(vc, false));
}
if (VCs.size() == 0) // everything is filtered out and we're filteredAreUncalled
return null;
// establish the baseline info from the first VC
final VariantContext first = VCs.get(0);
final String name = first.getSource();
final Allele refAllele = determineReferenceAllele(VCs);
final Set<Allele> alleles = new LinkedHashSet<Allele>();
final Set<String> filters = new TreeSet<String>();
final Map<String, Object> attributes = new TreeMap<String, Object>();
final Set<String> inconsistentAttributes = new HashSet<String>();
final Set<String> variantSources =
new HashSet<
String>(); // contains the set of sources we found in our set of VCs that are variant
final Set<String> rsIDs = new LinkedHashSet<String>(1); // most of the time there's one id
GenomeLoc loc = getLocation(genomeLocParser, first);
int depth = 0;
int maxAC = -1;
final Map<String, Object> attributesWithMaxAC = new TreeMap<String, Object>();
double log10PError = 1;
VariantContext vcWithMaxAC = null;
GenotypesContext genotypes = GenotypesContext.create();
// counting the number of filtered and variant VCs
int nFiltered = 0;
boolean remapped = false;
// cycle through and add info from the other VCs, making sure the loc/reference matches
for (VariantContext vc : VCs) {
if (loc.getStart() != vc.getStart()) // || !first.getReference().equals(vc.getReference()) )
throw new ReviewedStingException(
"BUG: attempting to merge VariantContexts with different start sites: first="
+ first.toString()
+ " second="
+ vc.toString());
if (getLocation(genomeLocParser, vc).size() > loc.size())
loc = getLocation(genomeLocParser, vc); // get the longest location
nFiltered += vc.isFiltered() ? 1 : 0;
if (vc.isVariant()) variantSources.add(vc.getSource());
AlleleMapper alleleMapping = resolveIncompatibleAlleles(refAllele, vc, alleles);
remapped = remapped || alleleMapping.needsRemapping();
alleles.addAll(alleleMapping.values());
mergeGenotypes(
genotypes, vc, alleleMapping, genotypeMergeOptions == GenotypeMergeType.UNIQUIFY);
log10PError = Math.min(log10PError, vc.isVariant() ? vc.getLog10PError() : 1);
filters.addAll(vc.getFilters());
//
// add attributes
//
// special case DP (add it up) and ID (just preserve it)
//
if (vc.hasAttribute(VCFConstants.DEPTH_KEY))
depth += vc.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0);
if (vc.hasID()) rsIDs.add(vc.getID());
if (mergeInfoWithMaxAC && vc.hasAttribute(VCFConstants.ALLELE_COUNT_KEY)) {
String rawAlleleCounts = vc.getAttributeAsString(VCFConstants.ALLELE_COUNT_KEY, null);
// lets see if the string contains a , separator
if (rawAlleleCounts.contains(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR)) {
List<String> alleleCountArray =
Arrays.asList(
rawAlleleCounts
.substring(1, rawAlleleCounts.length() - 1)
.split(VCFConstants.INFO_FIELD_ARRAY_SEPARATOR));
for (String alleleCount : alleleCountArray) {
final int ac = Integer.valueOf(alleleCount.trim());
if (ac > maxAC) {
maxAC = ac;
vcWithMaxAC = vc;
}
}
} else {
final int ac = Integer.valueOf(rawAlleleCounts);
if (ac > maxAC) {
maxAC = ac;
vcWithMaxAC = vc;
}
}
}
for (Map.Entry<String, Object> p : vc.getAttributes().entrySet()) {
String key = p.getKey();
// if we don't like the key already, don't go anywhere
if (!inconsistentAttributes.contains(key)) {
boolean alreadyFound = attributes.containsKey(key);
Object boundValue = attributes.get(key);
boolean boundIsMissingValue =
alreadyFound && boundValue.equals(VCFConstants.MISSING_VALUE_v4);
if (alreadyFound && !boundValue.equals(p.getValue()) && !boundIsMissingValue) {
// we found the value but we're inconsistent, put it in the exclude list
// System.out.printf("Inconsistent INFO values: %s => %s and %s%n", key, boundValue,
// p.getValue());
inconsistentAttributes.add(key);
attributes.remove(key);
} else if (!alreadyFound || boundIsMissingValue) { // no value
// if ( vc != first ) System.out.printf("Adding key %s => %s%n", p.getKey(),
// p.getValue());
attributes.put(key, p.getValue());
}
}
}
}
// if we have more alternate alleles in the merged VC than in one or more of the
// original VCs, we need to strip out the GL/PLs (because they are no longer accurate), as well
// as allele-dependent attributes like AC,AF
for (VariantContext vc : VCs) {
if (vc.alleles.size() == 1) continue;
if (hasPLIncompatibleAlleles(alleles, vc.alleles)) {
if (!genotypes.isEmpty())
logger.warn(
String.format(
"Stripping PLs at %s due incompatible alleles merged=%s vs. single=%s",
genomeLocParser.createGenomeLoc(vc), alleles, vc.alleles));
genotypes = stripPLs(genotypes);
// this will remove stale AC,AF attributed from vc
calculateChromosomeCounts(vc, attributes, true);
break;
}
}
// take the VC with the maxAC and pull the attributes into a modifiable map
if (mergeInfoWithMaxAC && vcWithMaxAC != null) {
attributesWithMaxAC.putAll(vcWithMaxAC.getAttributes());
}
// if at least one record was unfiltered and we want a union, clear all of the filters
if ((filteredRecordMergeType == FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED
&& nFiltered != VCs.size())
|| filteredRecordMergeType == FilteredRecordMergeType.KEEP_UNCONDITIONAL) filters.clear();
if (annotateOrigin) { // we care about where the call came from
String setValue;
if (nFiltered == 0
&& variantSources.size() == priorityListOfVCs.size()) // nothing was unfiltered
setValue = MERGE_INTERSECTION;
else if (nFiltered == VCs.size()) // everything was filtered out
setValue = MERGE_FILTER_IN_ALL;
else if (variantSources.isEmpty()) // everyone was reference
setValue = MERGE_REF_IN_ALL;
else {
LinkedHashSet<String> s = new LinkedHashSet<String>();
for (VariantContext vc : VCs)
if (vc.isVariant())
s.add(vc.isFiltered() ? MERGE_FILTER_PREFIX + vc.getSource() : vc.getSource());
setValue = Utils.join("-", s);
}
if (setKey != null) {
attributes.put(setKey, setValue);
if (mergeInfoWithMaxAC && vcWithMaxAC != null) {
attributesWithMaxAC.put(setKey, vcWithMaxAC.getSource());
}
}
}
if (depth > 0) attributes.put(VCFConstants.DEPTH_KEY, String.valueOf(depth));
final String ID = rsIDs.isEmpty() ? VCFConstants.EMPTY_ID_FIELD : Utils.join(",", rsIDs);
final VariantContextBuilder builder = new VariantContextBuilder().source(name).id(ID);
builder.loc(loc.getContig(), loc.getStart(), loc.getStop());
builder.alleles(alleles);
builder.genotypes(genotypes);
builder.log10PError(log10PError);
builder.filters(filters).attributes(mergeInfoWithMaxAC ? attributesWithMaxAC : attributes);
// Trim the padded bases of all alleles if necessary
VariantContext merged = createVariantContextWithTrimmedAlleles(builder.make());
if (printMessages && remapped) System.out.printf("Remapped => %s%n", merged);
return merged;
}