This VE eval module isn't useful anymore.
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Ryan Poplin
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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
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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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.util.Analysis;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.variantcontext.Allele;
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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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import java.util.HashMap;
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/**
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* @author rpoplin
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* @since Apr 6, 2010
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*/
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//@Analysis(name = "Variant Quality Score", description = "Shows various stats of sets of variants binned by variant quality score")
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@Deprecated
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public class VariantQualityScore {
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// TODO - this should really be a stratification
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// public class VariantQualityScore extends VariantEvaluator {
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//
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// // a mapping from quality score histogram bin to Ti/Tv ratio
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// @DataPoint(description = "the Ti/Tv ratio broken out by variant quality")
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// TiTvStats titvStats = null;
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//
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// @DataPoint(description = "average variant quality for each allele count")
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// AlleleCountStats alleleCountStats = null;
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//
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// static class TiTvStats extends TableType {
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// final static int NUM_BINS = 20;
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// final HashMap<Integer, Pair<Long,Long>> qualByIsTransition = new HashMap<Integer, Pair<Long,Long>>(); // A hashMap holds all the qualities until we are able to bin them appropriately
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// final long transitionByQuality[] = new long[NUM_BINS];
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// final long transversionByQuality[] = new long[NUM_BINS];
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// final double titvByQuality[] = new double[NUM_BINS]; // the final ti/tv sets that get reported out
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//
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// public Object[] getRowKeys() {
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// return new String[]{"sample"};
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// }
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//
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// public Object[] getColumnKeys() {
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// final String columnKeys[] = new String[NUM_BINS];
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// for( int iii = 0; iii < NUM_BINS; iii++ ) {
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// columnKeys[iii] = "titvBin" + iii;
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// }
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// return columnKeys;
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// }
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//
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// public String getCell(int x, int y) {
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// return String.valueOf(titvByQuality[y]);
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// }
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//
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// public String toString() {
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// StringBuffer returnString = new StringBuffer();
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// // output the ti/tv array
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// returnString.append("titvByQuality: ");
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// for( int iii = 0; iii < NUM_BINS; iii++ ) {
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// returnString.append(titvByQuality[iii]);
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// returnString.append(" ");
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// }
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// return returnString.toString();
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// }
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//
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// public void incrValue( final double qual, final boolean isTransition ) {
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// final Integer qualKey = Math.round((float) qual);
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// final long numTransition = (isTransition ? 1L : 0L);
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// final long numTransversion = (isTransition ? 0L : 1L);
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// if( qualByIsTransition.containsKey(qualKey) ) {
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// Pair<Long,Long> transitionPair = qualByIsTransition.get(qualKey);
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// transitionPair.set(transitionPair.getFirst() + numTransition, transitionPair.getSecond() + numTransversion);
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// qualByIsTransition.put(qualKey, transitionPair);
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// } else {
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// qualByIsTransition.put(qualKey, new Pair<Long,Long>(numTransition,numTransversion));
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// }
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// }
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//
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// public void organizeTiTvTables() {
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// for( int iii = 0; iii < NUM_BINS; iii++ ) {
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// transitionByQuality[iii] = 0L;
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// transversionByQuality[iii] = 0L;
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// titvByQuality[iii] = 0.0;
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// }
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//
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// int maxQual = 0;
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//
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// // Calculate the maximum quality score in order to normalize and histogram
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// for( final Integer qual : qualByIsTransition.keySet() ) {
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// if( qual > maxQual ) {
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// maxQual = qual;
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// }
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// }
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//
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// final double binSize = ((double)maxQual) / ((double) (NUM_BINS-1));
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//
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// for( final Integer qual : qualByIsTransition.keySet() ) {
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// final int index = (int)Math.floor( ((double) qual) / binSize );
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// if( index >= 0 ) { // BUGBUG: why is there overflow here?
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// Pair<Long,Long> transitionPair = qualByIsTransition.get(qual);
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// transitionByQuality[index] += transitionPair.getFirst();
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// transversionByQuality[index] += transitionPair.getSecond();
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// }
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// }
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//
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// for( int iii = 0; iii < NUM_BINS; iii++ ) {
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// if( transitionByQuality[iii] + transversionByQuality[iii] > 800L ) { // need to have a sufficient number of variants to get a useful Ti/Tv ratio
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// titvByQuality[iii] = ((double) transitionByQuality[iii]) / ((double) transversionByQuality[iii]);
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// } else {
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// titvByQuality[iii] = 0.0;
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// }
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// }
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//
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// }
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// }
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//
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// class AlleleCountStats extends TableType {
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// final HashMap<Integer, ArrayList<Double>> qualityListMap = new HashMap<Integer, ArrayList<Double>>();
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// final HashMap<Integer, Double> qualityMap = new HashMap<Integer, Double>();
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//
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// public Object[] getRowKeys() {
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// final int NUM_BINS = qualityListMap.keySet().size();
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// final String rowKeys[] = new String[NUM_BINS];
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// int iii = 0;
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// for( final Integer key : qualityListMap.keySet() ) {
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// rowKeys[iii] = "AC" + key;
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// iii++;
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// }
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// return rowKeys;
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//
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// }
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//
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// public Object[] getColumnKeys() {
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// return new String[]{"alleleCount","avgQual"};
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// }
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//
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// public String getCell(int x, int y) {
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// int iii = 0;
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// for( final Integer key : qualityListMap.keySet() ) {
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// if(iii == x) {
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// if(y == 0) { return String.valueOf(key); }
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// else { return String.valueOf(qualityMap.get(key)); }
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// }
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// iii++;
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// }
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// return null;
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// }
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//
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// public String toString() {
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// String returnString = "";
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// // output the quality map
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// returnString += "AlleleCountStats: ";
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// //for( int iii = 0; iii < NUM_BINS; iii++ ) {
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// // returnString += titvByQuality[iii] + " ";
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// //}
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// return returnString;
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// }
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//
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// public void incrValue( final double qual, final int alleleCount ) {
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// ArrayList<Double> list = qualityListMap.get(alleleCount);
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// if(list==null) { list = new ArrayList<Double>(); }
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// list.add(qual);
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// qualityListMap.put(alleleCount, list);
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// }
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//
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// public void organizeAlleleCountTables() {
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// for( final Integer key : qualityListMap.keySet() ) {
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// final ArrayList<Double> list = qualityListMap.get(key);
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// double meanQual = 0.0;
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// final double numQuals = (double)list.size();
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// for( Double qual : list ) {
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// meanQual += qual / numQuals;
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// }
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// qualityMap.put(key, meanQual);
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// }
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// }
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// }
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//
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// //public VariantQualityScore(VariantEvalWalker parent) {
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// //super(parent);
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// //}
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//
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// public String getName() {
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// return "VariantQualityScore";
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// }
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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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//
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// public String toString() {
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// return getName();
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// }
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//
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// public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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// final String interesting = null;
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//
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// if( eval != null && eval.isSNP() && eval.isBiallelic() && eval.isPolymorphicInSamples() ) { //BUGBUG: only counting biallelic sites (revisit what to do with triallelic sites)
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// if( titvStats == null ) { titvStats = new TiTvStats(); }
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// titvStats.incrValue(eval.getPhredScaledQual(), VariantContextUtils.isTransition(eval));
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//
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// if( alleleCountStats == null ) { alleleCountStats = new AlleleCountStats(); }
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// int alternateAlleleCount = 0;
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// for (final Allele a : eval.getAlternateAlleles()) {
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// alternateAlleleCount += eval.getCalledChrCount(a);
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// }
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// alleleCountStats.incrValue(eval.getPhredScaledQual(), alternateAlleleCount);
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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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//
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// public void finalizeEvaluation() {
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// if( titvStats != null ) {
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// titvStats.organizeTiTvTables();
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// }
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// if( alleleCountStats != null ) {
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// alleleCountStats.organizeAlleleCountTables();
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// }
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// }
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}
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