/** Initialize the stratifications, evaluations, evaluation contexts, and reporting object */
public void initialize() {
// Just list the modules, and exit quickly.
if (LIST) {
variantEvalUtils.listModulesAndExit();
}
// maintain the full list of comps
comps.addAll(compsProvided);
if (dbsnp.dbsnp.isBound()) {
comps.add(dbsnp.dbsnp);
knowns.add(dbsnp.dbsnp);
}
// Add a dummy comp track if none exists
if (comps.size() == 0)
comps.add(
new RodBinding<VariantContext>(VariantContext.class, "none", "UNBOUND", "", new Tags()));
// Set up set of additional knowns
for (RodBinding<VariantContext> compRod : comps) {
if (KNOWN_NAMES.contains(compRod.getName())) knowns.add(compRod);
}
// Now that we have all the rods categorized, determine the sample list from the eval rods.
Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), evals);
Set<String> vcfSamples =
SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
// Load the sample list
sampleNamesForEvaluation.addAll(
SampleUtils.getSamplesFromCommandLineInput(vcfSamples, SAMPLE_EXPRESSIONS));
numSamples = NUM_SAMPLES > 0 ? NUM_SAMPLES : sampleNamesForEvaluation.size();
if (Arrays.asList(STRATIFICATIONS_TO_USE).contains("Sample")) {
sampleNamesForStratification.addAll(sampleNamesForEvaluation);
}
sampleNamesForStratification.add(ALL_SAMPLE_NAME);
// Initialize select expressions
for (VariantContextUtils.JexlVCMatchExp jexl :
VariantContextUtils.initializeMatchExps(SELECT_NAMES, SELECT_EXPS)) {
SortableJexlVCMatchExp sjexl = new SortableJexlVCMatchExp(jexl.name, jexl.exp);
jexlExpressions.add(sjexl);
}
// Initialize the set of stratifications and evaluations to use
stratificationObjects =
variantEvalUtils.initializeStratificationObjects(
this, NO_STANDARD_STRATIFICATIONS, STRATIFICATIONS_TO_USE);
Set<Class<? extends VariantEvaluator>> evaluationObjects =
variantEvalUtils.initializeEvaluationObjects(NO_STANDARD_MODULES, MODULES_TO_USE);
for (VariantStratifier vs : getStratificationObjects()) {
if (vs.getName().equals("Filter")) byFilterIsEnabled = true;
else if (vs.getName().equals("Sample")) perSampleIsEnabled = true;
}
if (intervalsFile != null) {
boolean fail = true;
for (final VariantStratifier vs : stratificationObjects) {
if (vs.getClass().equals(IntervalStratification.class)) fail = false;
}
if (fail)
throw new UserException.BadArgumentValue(
"ST", "stratIntervals argument provided but -ST IntervalStratification not provided");
}
// Initialize the evaluation contexts
evaluationContexts =
variantEvalUtils.initializeEvaluationContexts(
stratificationObjects, evaluationObjects, null, null);
// Initialize report table
report = variantEvalUtils.initializeGATKReport(stratificationObjects, evaluationObjects);
// Load ancestral alignments
if (ancestralAlignmentsFile != null) {
try {
ancestralAlignments = new IndexedFastaSequenceFile(ancestralAlignmentsFile);
} catch (FileNotFoundException e) {
throw new ReviewedStingException(
String.format(
"The ancestral alignments file, '%s', could not be found",
ancestralAlignmentsFile.getAbsolutePath()));
}
}
// initialize CNVs
if (knownCNVsFile != null) {
knownCNVsByContig = createIntervalTreeByContig(knownCNVsFile);
}
}
/** 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;
}
/** 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;
}