private VariantContext findMatchingComp(
final VariantContext eval, final Collection<VariantContext> comps) {
// if no comps, return null
if (comps == null || comps.isEmpty()) return null;
// if no eval, return any comp
if (eval == null) return comps.iterator().next();
// find all of the matching comps
VariantContext lenientMatch = null;
for (final VariantContext comp : comps) {
switch (doEvalAndCompMatch(comp, eval, requireStrictAlleleMatch)) {
case STRICT:
return comp;
case LENIENT:
if (lenientMatch == null) lenientMatch = comp;
break;
case NO_MATCH:
// do nothing
}
}
// nothing matched, just return lenientMatch, which might be null
return lenientMatch;
}
/**
* this is the function that the inheriting class can expect to have called when the command line
* system has initialized.
*
* @return the return code to exit the program with
*/
protected int execute() throws Exception {
engine.setParser(parser);
argumentSources.add(this);
Walker<?, ?> walker = engine.getWalkerByName(getAnalysisName());
try {
// Make sure a valid GATK user key is present, if required.
authorizeGATKRun();
engine.setArguments(getArgumentCollection());
// File lists can require a bit of additional expansion. Set these explicitly by the engine.
engine.setSAMFileIDs(
ListFileUtils.unpackBAMFileList(getArgumentCollection().samFiles, parser));
engine.setWalker(walker);
walker.setToolkit(engine);
Collection<ReadFilter> filters = engine.createFilters();
engine.setFilters(filters);
// load the arguments into the walker / filters.
// TODO: The fact that this extra load call exists here when all the parsing happens at the
// engine
// TODO: level indicates that we're doing something wrong. Turn this around so that the GATK
// can drive
// TODO: argument processing.
loadArgumentsIntoObject(walker);
argumentSources.add(walker);
Collection<RMDTriplet> rodBindings =
ListFileUtils.unpackRODBindings(parser.getRodBindings(), parser);
engine.setReferenceMetaDataFiles(rodBindings);
for (ReadFilter filter : filters) {
loadArgumentsIntoObject(filter);
argumentSources.add(filter);
}
engine.execute();
generateGATKRunReport(walker);
} catch (Exception e) {
generateGATKRunReport(walker, e);
throw e;
}
// always return 0
return 0;
}
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;
}
/**
* 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.
}
/**
* GATK provides the walker as an argument source.
*
* @return List of walkers to load dynamically.
*/
@Override
protected Class[] getArgumentSources() {
// No walker info? No plugins.
if (getAnalysisName() == null) return new Class[] {};
Collection<Class> argumentSources = new ArrayList<Class>();
Walker walker = engine.getWalkerByName(getAnalysisName());
engine.setArguments(getArgumentCollection());
engine.setWalker(walker);
walker.setToolkit(engine);
argumentSources.add(walker.getClass());
Collection<ReadFilter> filters = engine.createFilters();
for (ReadFilter filter : filters) argumentSources.add(filter.getClass());
Class[] argumentSourcesAsArray = new Class[argumentSources.size()];
return argumentSources.toArray(argumentSourcesAsArray);
}
/** Collect relevant information from each variant in the supplied VCFs */
@Override
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
for (NewEvaluationContext nec : evaluationContexts.values()) {
synchronized (nec) {
nec.update0(tracker, ref, context);
}
}
if (tracker != null) {
String aastr =
(ancestralAlignments == null)
? null
: new String(
ancestralAlignments
.getSubsequenceAt(
ref.getLocus().getContig(),
ref.getLocus().getStart(),
ref.getLocus().getStop())
.getBases());
// --------- track --------- sample - VariantContexts -
HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>> evalVCs =
variantEvalUtils.bindVariantContexts(
tracker, ref, evals, byFilterIsEnabled, true, perSampleIsEnabled, mergeEvals);
HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>> compVCs =
variantEvalUtils.bindVariantContexts(
tracker, ref, comps, byFilterIsEnabled, false, false, false);
// for each eval track
for (final RodBinding<VariantContext> evalRod : evals) {
final Map<String, Collection<VariantContext>> emptyEvalMap = Collections.emptyMap();
final Map<String, Collection<VariantContext>> evalSet =
evalVCs.containsKey(evalRod) ? evalVCs.get(evalRod) : emptyEvalMap;
// for each sample stratifier
for (final String sampleName : sampleNamesForStratification) {
Collection<VariantContext> evalSetBySample = evalSet.get(sampleName);
if (evalSetBySample == null) {
evalSetBySample = new HashSet<VariantContext>(1);
evalSetBySample.add(null);
}
// for each eval in the track
for (VariantContext eval : evalSetBySample) {
// deal with ancestral alleles if requested
if (eval != null && aastr != null) {
eval = new VariantContextBuilder(eval).attribute("ANCESTRALALLELE", aastr).make();
}
// for each comp track
for (final RodBinding<VariantContext> compRod : comps) {
// no sample stratification for comps
final HashMap<String, Collection<VariantContext>> compSetHash = compVCs.get(compRod);
final Collection<VariantContext> compSet =
(compSetHash == null || compSetHash.size() == 0)
? Collections.<VariantContext>emptyList()
: compVCs.get(compRod).values().iterator().next();
// find the comp
final VariantContext comp = findMatchingComp(eval, compSet);
HashMap<VariantStratifier, List<String>> stateMap =
new HashMap<VariantStratifier, List<String>>();
for (VariantStratifier vs : stratificationObjects) {
List<String> states =
vs.getRelevantStates(
ref, tracker, comp, compRod.getName(), eval, evalRod.getName(), sampleName);
stateMap.put(vs, states);
}
ArrayList<StateKey> stateKeys = new ArrayList<StateKey>();
variantEvalUtils.initializeStateKeys(stateMap, null, null, stateKeys);
HashSet<StateKey> stateKeysHash = new HashSet<StateKey>(stateKeys);
for (StateKey stateKey : stateKeysHash) {
NewEvaluationContext nec = evaluationContexts.get(stateKey);
// eval against the comp
synchronized (nec) {
nec.apply(tracker, ref, context, comp, eval);
}
// eval=null against all comps of different type that aren't bound to another eval
for (VariantContext otherComp : compSet) {
if (otherComp != comp && !compHasMatchingEval(otherComp, evalSetBySample)) {
synchronized (nec) {
nec.apply(tracker, ref, context, otherComp, null);
}
}
}
}
}
}
}
if (mergeEvals) break; // stop processing the eval tracks
}
}
return null;
}
/**
* Subset VC record if necessary and emit the modified record (provided it satisfies criteria for
* printing)
*
* @param tracker the ROD tracker
* @param ref reference information
* @param context alignment info
* @return 1 if the record was printed to the output file, 0 if otherwise
*/
@Override
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (tracker == null) return 0;
Collection<VariantContext> vcs =
tracker.getValues(variantCollection.variants, context.getLocation());
if (vcs == null || vcs.size() == 0) {
return 0;
}
for (VariantContext vc : vcs) {
if (MENDELIAN_VIOLATIONS) {
boolean foundMV = false;
for (MendelianViolation mv : mvSet) {
if (mv.isViolation(vc)) {
foundMV = true;
// System.out.println(vc.toString());
if (outMVFile != null)
outMVFileStream.format(
"MV@%s:%d. REF=%s, ALT=%s, AC=%d, momID=%s, dadID=%s, childID=%s, momG=%s, momGL=%s, dadG=%s, dadGL=%s, "
+ "childG=%s childGL=%s\n",
vc.getChr(),
vc.getStart(),
vc.getReference().getDisplayString(),
vc.getAlternateAllele(0).getDisplayString(),
vc.getChromosomeCount(vc.getAlternateAllele(0)),
mv.getSampleMom(),
mv.getSampleDad(),
mv.getSampleChild(),
vc.getGenotype(mv.getSampleMom()).toBriefString(),
vc.getGenotype(mv.getSampleMom()).getLikelihoods().getAsString(),
vc.getGenotype(mv.getSampleDad()).toBriefString(),
vc.getGenotype(mv.getSampleMom()).getLikelihoods().getAsString(),
vc.getGenotype(mv.getSampleChild()).toBriefString(),
vc.getGenotype(mv.getSampleChild()).getLikelihoods().getAsString());
}
}
if (!foundMV) break;
}
if (DISCORDANCE_ONLY) {
Collection<VariantContext> compVCs =
tracker.getValues(discordanceTrack, context.getLocation());
if (!isDiscordant(vc, compVCs)) return 0;
}
if (CONCORDANCE_ONLY) {
Collection<VariantContext> compVCs =
tracker.getValues(concordanceTrack, context.getLocation());
if (!isConcordant(vc, compVCs)) return 0;
}
if (alleleRestriction.equals(NumberAlleleRestriction.BIALLELIC) && !vc.isBiallelic())
continue;
if (alleleRestriction.equals(NumberAlleleRestriction.MULTIALLELIC) && vc.isBiallelic())
continue;
if (!selectedTypes.contains(vc.getType())) continue;
VariantContext sub = subsetRecord(vc, samples);
if ((sub.isPolymorphic() || !EXCLUDE_NON_VARIANTS)
&& (!sub.isFiltered() || !EXCLUDE_FILTERED)) {
for (VariantContextUtils.JexlVCMatchExp jexl : jexls) {
if (!VariantContextUtils.match(sub, jexl)) {
return 0;
}
}
if (SELECT_RANDOM_NUMBER) {
randomlyAddVariant(++variantNumber, sub, ref.getBase());
} else if (!SELECT_RANDOM_FRACTION
|| (GenomeAnalysisEngine.getRandomGenerator().nextDouble() < fractionRandom)) {
vcfWriter.add(sub);
}
}
}
return 1;
}
/** Collect relevant information from each variant in the supplied VCFs */
@Override
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
// we track the processed bp and expose this for modules instead of wasting CPU power on
// calculating
// the same thing over and over in evals that want the processed bp
synchronized (this) {
nProcessedLoci += context.getSkippedBases() + (ref == null ? 0 : 1);
}
if (tracker != null) {
String aastr =
(ancestralAlignments == null)
? null
: new String(
ancestralAlignments
.getSubsequenceAt(
ref.getLocus().getContig(),
ref.getLocus().getStart(),
ref.getLocus().getStop())
.getBases());
// // update the dynamic stratifications
// for (final VariantContext vc : tracker.getValues(evals, ref.getLocus())) {
// // don't worry -- DynamicStratification only work with one eval object
// for ( final DynamicStratification ds : dynamicStratifications ) {
// ds.update(vc);
// }
// }
// --------- track --------- sample - VariantContexts -
HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>> evalVCs =
variantEvalUtils.bindVariantContexts(
tracker, ref, evals, byFilterIsEnabled, true, perSampleIsEnabled, mergeEvals);
HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>> compVCs =
variantEvalUtils.bindVariantContexts(
tracker, ref, comps, byFilterIsEnabled, false, false, false);
// for each eval track
for (final RodBinding<VariantContext> evalRod : evals) {
final Map<String, Collection<VariantContext>> emptyEvalMap = Collections.emptyMap();
final Map<String, Collection<VariantContext>> evalSet =
evalVCs.containsKey(evalRod) ? evalVCs.get(evalRod) : emptyEvalMap;
// for each sample stratifier
for (final String sampleName : sampleNamesForStratification) {
Collection<VariantContext> evalSetBySample = evalSet.get(sampleName);
if (evalSetBySample == null) {
evalSetBySample = new HashSet<VariantContext>(1);
evalSetBySample.add(null);
}
// for each eval in the track
for (VariantContext eval : evalSetBySample) {
// deal with ancestral alleles if requested
if (eval != null && aastr != null) {
eval = new VariantContextBuilder(eval).attribute("ANCESTRALALLELE", aastr).make();
}
// for each comp track
for (final RodBinding<VariantContext> compRod : comps) {
// no sample stratification for comps
final HashMap<String, Collection<VariantContext>> compSetHash = compVCs.get(compRod);
final Collection<VariantContext> compSet =
(compSetHash == null || compSetHash.size() == 0)
? Collections.<VariantContext>emptyList()
: compVCs.get(compRod).values().iterator().next();
// find the comp
final VariantContext comp = findMatchingComp(eval, compSet);
for (EvaluationContext nec :
getEvaluationContexts(
tracker, ref, eval, evalRod.getName(), comp, compRod.getName(), sampleName)) {
// eval against the comp
synchronized (nec) {
nec.apply(tracker, ref, context, comp, eval);
}
// eval=null against all comps of different type that aren't bound to another eval
for (VariantContext otherComp : compSet) {
if (otherComp != comp && !compHasMatchingEval(otherComp, evalSetBySample)) {
synchronized (nec) {
nec.apply(tracker, ref, context, otherComp, null);
}
}
}
}
}
}
}
if (mergeEvals) break; // stop processing the eval tracks
}
}
return null;
}