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VariantEval optimization 

-- Use a LinkedHashMap not a TreeMap so iteration is faster.
-- Note that with a lot of stratifications the update0 is taking up a lot of time.  For example, with 822 samples and functional class and sample on there are 100K contexts and 30% of the runtime is just in the update0 call
This commit is contained in:
Mark DePristo 2012-03-22 22:13:24 -04:00
parent a0602e534c
commit fee8d86f63
3 changed files with 10 additions and 22 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -326,7 +326,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
*/ */
@Override @Override
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
for ( NewEvaluationContext nec : evaluationContexts.values() ) { for ( final NewEvaluationContext nec : evaluationContexts.values() ) {
synchronized (nec) { synchronized (nec) {
nec.update0(tracker, ref, context); nec.update0(tracker, ref, context);
} }

28
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/NewEvaluationContext.java
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@ -10,29 +10,17 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException; import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.variantcontext.VariantContext; import org.broadinstitute.sting.utils.variantcontext.VariantContext;
import java.util.HashMap; import java.util.*;
import java.util.Set;
import java.util.TreeMap;
public class NewEvaluationContext extends HashMap<VariantStratifier, String> { public class NewEvaluationContext extends HashMap<VariantStratifier, String> {
public TreeMap<String, VariantEvaluator> evaluationInstances; private Map<String, VariantEvaluator> evaluationInstances;
public String toString() {
String value = "";
for ( VariantStratifier key : this.keySet() ) {
value += "\t" + key.getName() + ":" + this.get(key) + "\n";
}
return value;
}
public void addEvaluationClassList(VariantEvalWalker walker, StateKey stateKey, Set<Class<? extends VariantEvaluator>> evaluationClasses) { public void addEvaluationClassList(VariantEvalWalker walker, StateKey stateKey, Set<Class<? extends VariantEvaluator>> evaluationClasses) {
evaluationInstances = new TreeMap<String, VariantEvaluator>(); evaluationInstances = new LinkedHashMap<String, VariantEvaluator>(evaluationClasses.size());
for ( Class<? extends VariantEvaluator> c : evaluationClasses ) { for ( final Class<? extends VariantEvaluator> c : evaluationClasses ) {
try { try {
VariantEvaluator eval = c.newInstance(); final VariantEvaluator eval = c.newInstance();
eval.initialize(walker); eval.initialize(walker);
if (eval.stateIsApplicable(stateKey)) { if (eval.stateIsApplicable(stateKey)) {
@ -47,11 +35,11 @@ public class NewEvaluationContext extends HashMap<VariantStratifier, String> {
} }
public TreeMap<String, VariantEvaluator> getEvaluationClassList() { public TreeMap<String, VariantEvaluator> getEvaluationClassList() {
return evaluationInstances; return new TreeMap<String, VariantEvaluator>(evaluationInstances);
} }
public void apply(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantContext comp, VariantContext eval) { public void apply(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantContext comp, VariantContext eval) {
for ( VariantEvaluator evaluation : evaluationInstances.values() ) { for ( final VariantEvaluator evaluation : evaluationInstances.values() ) {
// we always call update0 in case the evaluation tracks things like number of bases covered // we always call update0 in case the evaluation tracks things like number of bases covered
// the other updateN methods don't see a null context // the other updateN methods don't see a null context
@ -79,7 +67,7 @@ public class NewEvaluationContext extends HashMap<VariantStratifier, String> {
} }
public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
for ( VariantEvaluator evaluation : evaluationInstances.values() ) { for ( final VariantEvaluator evaluation : evaluationInstances.values() ) {
evaluation.update0(tracker, ref, context); evaluation.update0(tracker, ref, context);
} }
} }

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
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@ -191,7 +191,7 @@ public class VariantEvalUtils {
* @return a map of all the evaluation contexts * @return a map of all the evaluation contexts
*/ */
public HashMap<StateKey, NewEvaluationContext> initializeEvaluationContexts(Set<VariantStratifier> stratificationObjects, Set<Class<? extends VariantEvaluator>> evaluationObjects, Stack<VariantStratifier> stratStack, NewEvaluationContext ec) { public HashMap<StateKey, NewEvaluationContext> initializeEvaluationContexts(Set<VariantStratifier> stratificationObjects, Set<Class<? extends VariantEvaluator>> evaluationObjects, Stack<VariantStratifier> stratStack, NewEvaluationContext ec) {
HashMap<StateKey, NewEvaluationContext> ecs = new HashMap<StateKey, NewEvaluationContext>(); HashMap<StateKey, NewEvaluationContext> ecs = new LinkedHashMap<StateKey, NewEvaluationContext>();
if (stratStack == null) { if (stratStack == null) {
stratStack = new Stack<VariantStratifier>(); stratStack = new Stack<VariantStratifier>();