Caching getSimpleName() in VariantEval is a big performance improvement
-- Removed the SimpleMetricsByAC table, as one should just use the AlleleCount Stratefication and the upcoming VariantSummary table
This commit is contained in:
Mark DePristo
parent
a3aef8fa53
commit
6c2555885c
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@ -265,9 +265,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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stratificationObjects = variantEvalUtils.initializeStratificationObjects(this, NO_STANDARD_STRATIFICATIONS, STRATIFICATIONS_TO_USE);
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Set<Class<? extends VariantEvaluator>> evaluationObjects = variantEvalUtils.initializeEvaluationObjects(NO_STANDARD_MODULES, MODULES_TO_USE);
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for ( VariantStratifier vs : getStratificationObjects() ) {
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if ( vs.getClass().getSimpleName().equals("Filter") )
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if ( vs.getName().equals("Filter") )
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byFilterIsEnabled = true;
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else if ( vs.getClass().getSimpleName().equals("Sample") )
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else if ( vs.getName().equals("Sample") )
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perSampleIsEnabled = true;
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}
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@ -458,9 +458,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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table.addColumn(subTableName, subTableName);
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for ( VariantStratifier vs : stratificationObjects ) {
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String columnName = vs.getClass().getSimpleName();
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table.addColumn(columnName, "unknown");
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table.addColumn(vs.getName(), "unknown");
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}
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table.addColumn("row", "unknown");
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@ -484,9 +482,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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String r = (String) t.getRowKeys()[row];
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for ( VariantStratifier vs : stratificationObjects ) {
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String columnName = vs.getClass().getSimpleName();
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table.set(stateKey.toString() + r, columnName, stateKey.get(vs.getClass().getSimpleName()));
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final String columnName = vs.getName();
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table.set(stateKey.toString() + r, columnName, stateKey.get(columnName));
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}
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for (int col = 0; col < t.getColumnKeys().length; col++) {
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@ -507,9 +504,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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GATKReportTable table = report.getTable(ve.getClass().getSimpleName());
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for ( VariantStratifier vs : stratificationObjects ) {
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String columnName = vs.getClass().getSimpleName();
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String columnName = vs.getName();
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table.set(stateKey.toString(), columnName, stateKey.get(vs.getClass().getSimpleName()));
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table.set(stateKey.toString(), columnName, stateKey.get(vs.getName()));
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}
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table.set(stateKey.toString(), field.getName(), field.get(ve));
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@ -1,194 +0,0 @@
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package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
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import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Degeneracy;
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import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Sample;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.StateKey;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
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import java.util.ArrayList;
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/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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/**
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* @author depristo
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* @since Apr 11, 2010
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*/
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@Analysis(name = "Quality Metrics by allele count", description = "Shows various stats binned by allele count")
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public class SimpleMetricsByAC extends VariantEvaluator implements StandardEval {
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// a mapping from quality score histogram bin to Ti/Tv ratio
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@DataPoint(description = "TiTv by allele count")
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MetricsByAc metrics = null;
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private final static Object[] METRIC_COLUMNS = {"AC", "nTi", "nTv", "n", "TiTv"};
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private int numSamples;
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class MetricsAtAC {
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public int ac = -1, nTi = 0, nTv = 0;
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public MetricsAtAC(int ac) { this.ac = ac; }
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public void update(VariantContext eval) {
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if ( VariantContextUtils.isTransition(eval) )
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nTi++;
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else
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nTv++;
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}
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// corresponding to METRIC_COLUMNS
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public String getColumn(int i) {
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switch (i) {
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case 0: return String.valueOf(ac);
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case 1: return String.valueOf(nTi);
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case 2: return String.valueOf(nTv);
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case 3: return String.valueOf(nTi + nTv);
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case 4: return String.valueOf(ratio(nTi, nTv));
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default:
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throw new ReviewedStingException("Unexpected column " + i);
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}
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}
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}
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class MetricsByAc implements TableType {
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ArrayList<MetricsAtAC> metrics = new ArrayList<MetricsAtAC>();
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Object[] rows = null;
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public MetricsByAc( int nchromosomes ) {
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rows = new Object[nchromosomes+1];
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metrics = new ArrayList<MetricsAtAC>(nchromosomes+1);
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for ( int i = 0; i < nchromosomes + 1; i++ ) {
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metrics.add(new MetricsAtAC(i));
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rows[i] = "ac" + i;
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}
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}
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public Object[] getRowKeys() {
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return rows;
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}
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public Object[] getColumnKeys() {
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return METRIC_COLUMNS;
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}
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public String getName() {
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return "MetricsByAc";
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}
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public String getCell(int ac, int y) {
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return metrics.get(ac).getColumn(y);
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}
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public String toString() {
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return "";
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}
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public void incrValue( VariantContext eval ) {
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int ac = -1;
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if ( eval.hasGenotypes() )
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ac = eval.getCalledChrCount(eval.getAlternateAllele(0));
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else if ( eval.hasAttribute("AC") ) {
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ac = eval.getAttributeAsInt("AC", -1);
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}
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if ( ac != -1 ) {
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metrics.get(ac).update(eval);
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}
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}
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}
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public void initialize(VariantEvalWalker walker) {
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numSamples = walker.getNumSamples();
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metrics = new MetricsByAc(2*numSamples);
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}
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public String getName() {
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return "SimpleMetricsByAC";
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}
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public int getComparisonOrder() {
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return 1; // we only need to see each eval track
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}
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public boolean enabled() {
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return true;
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}
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public String toString() {
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return getName();
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}
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public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if (numSamples == 0) {
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return null;
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}
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final String interesting = null;
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if (eval != null) {
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if ( metrics == null ) {
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int nSamples = numSamples;
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if ( nSamples != -1 ) {
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metrics = new MetricsByAc(2 * nSamples);
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}
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}
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if ( eval.isSNP() && eval.isBiallelic() && eval.isPolymorphicInSamples() && metrics != null ) {
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metrics.incrValue(eval);
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}
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}
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return interesting; // This module doesn't capture any interesting sites, so return null
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}
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@Override
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public boolean stateIsApplicable(StateKey stateKey) {
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String sampleClassName = Sample.class.getSimpleName();
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String degeneracyClassName = Degeneracy.class.getSimpleName();
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//return !(stateKey.containsKey(sampleClassName) && !stateKey.get(sampleClassName).equalsIgnoreCase("all"));
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if (stateKey.containsKey(sampleClassName) && !stateKey.get(sampleClassName).equalsIgnoreCase("all")) {
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return false;
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}
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if (stateKey.containsKey(degeneracyClassName) && !stateKey.get(degeneracyClassName).equalsIgnoreCase("all")) {
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return false;
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}
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return true;
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}
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}
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@ -9,10 +9,15 @@ import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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public abstract class VariantStratifier implements Comparable {
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public abstract class VariantStratifier implements Comparable<VariantStratifier> {
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private VariantEvalWalker variantEvalWalker;
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final private String name;
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protected ArrayList<String> states = new ArrayList<String>();
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protected VariantStratifier() {
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name = this.getClass().getSimpleName();
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}
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/**
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* @return a reference to the parent VariantEvalWalker running this stratification
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*/
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@ -34,8 +39,12 @@ public abstract class VariantStratifier implements Comparable {
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return null;
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}
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public int compareTo(Object o1) {
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return this.getClass().getSimpleName().compareTo(o1.getClass().getSimpleName());
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public int compareTo(VariantStratifier o1) {
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return this.getName().compareTo(o1.getName());
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}
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public final String getName() {
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return name;
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}
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public ArrayList<String> getAllStates() {
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@ -21,7 +21,7 @@ public class NewEvaluationContext extends HashMap<VariantStratifier, String> {
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String value = "";
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for ( VariantStratifier key : this.keySet() ) {
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value += "\t" + key.getClass().getSimpleName() + ":" + this.get(key) + "\n";
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value += "\t" + key.getName() + ":" + this.get(key) + "\n";
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}
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return value;
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@ -1,24 +1,23 @@
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package org.broadinstitute.sting.gatk.walkers.varianteval.util;
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import java.util.Map;
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import java.util.TreeMap;
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public class StateKey extends TreeMap<String, String> {
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public int hashCode() {
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int hashCode = 1;
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for (String key : this.keySet()) {
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String value = this.get(key);
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hashCode *= key.hashCode() + value.hashCode();
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}
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return hashCode;
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}
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// public int hashCode() {
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// int hashCode = 1;
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//
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// for (final Map.Entry<String,String> pair : this.entrySet()) {
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// hashCode *= pair.getKey().hashCode() + pair.getValue().hashCode();
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// }
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//
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// return hashCode;
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// }
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public String toString() {
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String value = "";
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for ( String key : this.keySet() ) {
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for ( final String key : this.keySet() ) {
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//value += "\tstate " + key + ":" + this.get(key) + "\n";
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value += String.format("%s:%s;", key, this.get(key));
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}
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@ -196,7 +196,7 @@ public class VariantEvalUtils {
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for (VariantStratifier vs : ec.keySet()) {
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String state = ec.get(vs);
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stateKey.put(vs.getClass().getSimpleName(), state);
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stateKey.put(vs.getName(), state);
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}
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ec.addEvaluationClassList(variantEvalWalker, stateKey, evaluationObjects);
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@ -230,7 +230,7 @@ public class VariantEvalUtils {
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table.addColumn(tableName, tableName);
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for (VariantStratifier vs : stratificationObjects) {
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String columnName = vs.getClass().getSimpleName();
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String columnName = vs.getName();
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table.addColumn(columnName, "unknown");
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}
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@ -410,7 +410,7 @@ public class VariantEvalUtils {
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newStateKey.putAll(stateKey);
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}
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newStateKey.put(vs.getClass().getSimpleName(), state);
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newStateKey.put(vs.getName(), state);
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initializeStateKeys(stateMap, newStateStack, newStateKey, stateKeys);
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}
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