Replace uses of NestedHashMap with NestedIntegerArray.
* Removed from codebase NestedHashMap since it is unused and untested. * Integration tests change because the BQSR CSV is now sorted automatically. * Resolves GSA-732
This commit is contained in:
Eric Banks
parent
4b1071a815
commit
69b8173535
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@ -46,6 +46,8 @@
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package org.broadinstitute.sting.utils.recalibration;
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import com.google.java.contract.Ensures;
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import com.google.java.contract.Requires;
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import net.sf.samtools.SAMFileHeader;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.gatk.report.GATKReport;
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@ -59,7 +61,6 @@ import org.broadinstitute.sting.utils.R.RScriptExecutor;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.classloader.PluginManager;
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import org.broadinstitute.sting.utils.collections.NestedIntegerArray;
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import org.broadinstitute.sting.utils.collections.NestedHashMap;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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@ -423,7 +424,7 @@ public class RecalUtils {
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private static void writeCSV(final PrintStream deltaTableFile, final RecalibrationTables recalibrationTables, final String recalibrationMode, final Covariate[] requestedCovariates, final boolean printHeader) {
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final NestedHashMap deltaTable = new NestedHashMap();
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final NestedIntegerArray<RecalDatum> deltaTable = createDeltaTable(recalibrationTables, requestedCovariates.length);
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// add the quality score table to the delta table
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final NestedIntegerArray<RecalDatum> qualTable = recalibrationTables.getQualityScoreTable();
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@ -470,24 +471,57 @@ public class RecalUtils {
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covariateNameMap.put(covariate, parseCovariateName(covariate));
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// print each data line
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for (final NestedHashMap.Leaf leaf : deltaTable.getAllLeaves()) {
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for (final NestedIntegerArray.Leaf<RecalDatum> leaf : deltaTable.getAllLeaves()) {
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final List<Object> deltaKeys = generateValuesFromKeys(leaf.keys, requestedCovariates, covariateNameMap);
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final RecalDatum deltaDatum = (RecalDatum)leaf.value;
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final RecalDatum deltaDatum = leaf.value;
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deltaTableFile.print(Utils.join(",", deltaKeys));
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deltaTableFile.print("," + deltaDatum.stringForCSV());
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deltaTableFile.println("," + recalibrationMode);
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}
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}
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protected static List<Object> generateValuesFromKeys(final List<Object> keys, final Covariate[] covariates, final Map<Covariate, String> covariateNameMap) {
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/*
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* Return an initialized nested integer array with appropriate dimensions for use with the delta tables
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*
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* @param recalibrationTables the recal tables
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* @param numCovariates the total number of covariates being used
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* @return a non-null nested integer array
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*/
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@Requires("recalibrationTables != null && numCovariates > 0")
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@Ensures("result != null")
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private static NestedIntegerArray<RecalDatum> createDeltaTable(final RecalibrationTables recalibrationTables, final int numCovariates) {
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final int[] dimensionsForDeltaTable = new int[4];
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// initialize the dimensions with those of the qual table to start with
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final NestedIntegerArray<RecalDatum> qualTable = recalibrationTables.getQualityScoreTable();
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final int[] dimensionsOfQualTable = qualTable.getDimensions();
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dimensionsForDeltaTable[0] = dimensionsOfQualTable[0]; // num read groups
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dimensionsForDeltaTable[1] = numCovariates + 1; // num covariates
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dimensionsForDeltaTable[2] = dimensionsOfQualTable[1];
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dimensionsForDeltaTable[3] = dimensionsOfQualTable[2];
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// now, update the dimensions based on the optional covariate tables as needed
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for ( int i = RecalibrationTables.TableType.OPTIONAL_COVARIATE_TABLES_START.ordinal(); i < numCovariates; i++ ) {
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final NestedIntegerArray<RecalDatum> covTable = recalibrationTables.getTable(i);
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final int[] dimensionsOfCovTable = covTable.getDimensions();
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dimensionsForDeltaTable[2] = Math.max(dimensionsForDeltaTable[2], dimensionsOfCovTable[2]);
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dimensionsForDeltaTable[3] = Math.max(dimensionsForDeltaTable[3], dimensionsOfCovTable[3]);
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}
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return new NestedIntegerArray<RecalDatum>(dimensionsForDeltaTable);
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}
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protected static List<Object> generateValuesFromKeys(final int[] keys, final Covariate[] covariates, final Map<Covariate, String> covariateNameMap) {
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final List<Object> values = new ArrayList<Object>(4);
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values.add(covariates[RecalibrationTables.TableType.READ_GROUP_TABLE.ordinal()].formatKey((Integer)keys.get(0)));
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final int covariateIndex = (Integer)keys.get(1);
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values.add(covariates[RecalibrationTables.TableType.READ_GROUP_TABLE.ordinal()].formatKey(keys[0]));
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final int covariateIndex = keys[1];
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final int covariateKey = keys[2];
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final Covariate covariate = covariateIndex == covariates.length ? covariates[RecalibrationTables.TableType.QUALITY_SCORE_TABLE.ordinal()] : covariates[covariateIndex];
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final int covariateKey = (Integer)keys.get(2);
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values.add(covariate.formatKey(covariateKey));
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values.add(covariateNameMap.get(covariate));
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values.add(EventType.eventFrom((Integer)keys.get(3)).prettyPrint());
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values.add(EventType.eventFrom(keys[3]).prettyPrint());
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return values;
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}
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@ -501,20 +535,14 @@ public class RecalUtils {
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* @param deltaKey the key to the table
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* @param recalDatum the recal datum to combine with the accuracyDatum element in the table
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*/
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private static void addToDeltaTable(final NestedHashMap deltaTable, final int[] deltaKey, final RecalDatum recalDatum) {
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Object[] wrappedKey = wrapKeys(deltaKey);
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final RecalDatum deltaDatum = (RecalDatum)deltaTable.get(wrappedKey); // check if we already have a RecalDatum for this key
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private static void addToDeltaTable(final NestedIntegerArray<RecalDatum> deltaTable, final int[] deltaKey, final RecalDatum recalDatum) {
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final RecalDatum deltaDatum = deltaTable.get(deltaKey); // check if we already have a RecalDatum for this key
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if (deltaDatum == null)
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deltaTable.put(new RecalDatum(recalDatum), wrappedKey); // if we don't have a key yet, create a new one with the same values as the curent datum
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// if we don't have a key yet, create a new one with the same values as the current datum
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deltaTable.put(new RecalDatum(recalDatum), deltaKey);
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else
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deltaDatum.combine(recalDatum); // if we do have a datum, combine it with this one.
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}
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private static Object[] wrapKeys(final int[] keys) {
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final Object[] wrappedKeys = new Object[keys.length];
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for (int i = 0; i < keys.length; i++)
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wrappedKeys[i] = keys[i];
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return wrappedKeys;
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// if we do have a datum, combine it with this one
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deltaDatum.combine(recalDatum);
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}
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/**
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@ -151,7 +151,7 @@ public class BQSRIntegrationTest extends WalkerTest {
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" -sortAllCols" +
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" --plot_pdf_file /dev/null" +
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" --intermediate_csv_file %s",
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Arrays.asList("dd6e0e1e3f53f8ae0c8f5de21ded6ee9"));
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Arrays.asList("90ad19143024684e3c4410dc8fd2bd9d"));
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executeTest("testBQSR-CSVfile", spec);
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}
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@ -1,132 +0,0 @@
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/*
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* Copyright (c) 2012 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
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.utils.collections;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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/**
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* Created by IntelliJ IDEA.
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* User: rpoplin
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* Date: Dec 29, 2009
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*/
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public class NestedHashMap {
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public final Map data = new HashMap<Object, Object>();
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public Object get( final Object... keys ) {
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Map map = this.data;
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final int nestedMaps = keys.length - 1;
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for( int iii = 0; iii < nestedMaps; iii++ ) {
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map = (Map) map.get(keys[iii]);
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if( map == null ) { return null; }
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}
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return map.get(keys[nestedMaps]);
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}
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public synchronized void put( final Object value, final Object... keys ) { // WARNING! value comes before the keys!
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this.put(value, false, keys );
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}
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public synchronized Object put( final Object value, boolean keepOldBindingIfPresent, final Object... keys ) {
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Map map = this.data;
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final int keysLength = keys.length;
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for( int iii = 0; iii < keysLength; iii++ ) {
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if( iii == keysLength - 1 ) {
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if ( keepOldBindingIfPresent && map.containsKey(keys[iii]) ) {
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// this code test is for parallel protection when you call put() multiple times in different threads
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// to initialize the map. It returns the already bound key[iii] -> value
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return map.get(keys[iii]);
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} else {
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// we are a new binding, put it in the map
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map.put(keys[iii], value);
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return value;
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}
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} else {
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Map tmp = (Map) map.get(keys[iii]);
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if( tmp == null ) {
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tmp = new HashMap();
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map.put(keys[iii], tmp);
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}
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map = tmp;
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}
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}
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return value; // todo -- should never reach this point
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}
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public List<Object> getAllValues() {
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final List<Object> result = new ArrayList<Object>();
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fillAllValues(data, result);
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return result;
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}
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private void fillAllValues(final Map map, final List<Object> result) {
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for ( Object value : map.values() ) {
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if ( value == null )
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continue;
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if ( value instanceof Map )
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fillAllValues((Map)value, result);
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else
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result.add(value);
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}
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}
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public static class Leaf {
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public final List<Object> keys;
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public final Object value;
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public Leaf(final List<Object> keys, final Object value) {
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this.keys = keys;
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this.value = value;
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}
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}
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public List<Leaf> getAllLeaves() {
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final List<Leaf> result = new ArrayList<Leaf>();
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final List<Object> path = new ArrayList<Object>();
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fillAllLeaves(data, path, result);
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return result;
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}
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private void fillAllLeaves(final Map map, final List<Object> path, final List<Leaf> result) {
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for ( final Object key : map.keySet() ) {
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final Object value = map.get(key);
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if ( value == null )
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continue;
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final List<Object> newPath = new ArrayList<Object>(path);
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newPath.add(key);
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if ( value instanceof Map ) {
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fillAllLeaves((Map) value, newPath, result);
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} else {
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result.add(new Leaf(newPath, value));
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}
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}
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}
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}
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