diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java deleted file mode 100755 index 347ca56b8..000000000 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantQualityScore.java +++ /dev/null @@ -1,249 +0,0 @@ -/* - * Copyright (c) 2010 The Broad Institute - * - * Permission is hereby granted, free of charge, to any person - * obtaining a copy of this software and associated documentation - * files (the "Software"), to deal in the Software without - * restriction, including without limitation the rights to use, - * copy, modify, merge, publish, distribute, sublicense, and/or sell - * copies of the Software, and to permit persons to whom the - * Software is furnished to do so, subject to the following - * conditions: - * - * The above copyright notice and this permission notice shall be - * included in all copies or substantial portions of the Software. - * - * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES - * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND - * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT - * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, - * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING - * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR - * THE USE OR OTHER DEALINGS IN THE SOFTWARE. - */ - -package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators; - -import org.broadinstitute.sting.gatk.contexts.AlignmentContext; -import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis; -import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint; -import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.variantcontext.Allele; -import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; - -import java.util.ArrayList; -import java.util.HashMap; - -/** - * @author rpoplin - * @since Apr 6, 2010 - */ - -//@Analysis(name = "Variant Quality Score", description = "Shows various stats of sets of variants binned by variant quality score") -@Deprecated -public class VariantQualityScore { - // TODO - this should really be a stratification - -// public class VariantQualityScore extends VariantEvaluator { -// -// // a mapping from quality score histogram bin to Ti/Tv ratio -// @DataPoint(description = "the Ti/Tv ratio broken out by variant quality") -// TiTvStats titvStats = null; -// -// @DataPoint(description = "average variant quality for each allele count") -// AlleleCountStats alleleCountStats = null; -// -// static class TiTvStats extends TableType { -// final static int NUM_BINS = 20; -// final HashMap> qualByIsTransition = new HashMap>(); // A hashMap holds all the qualities until we are able to bin them appropriately -// final long transitionByQuality[] = new long[NUM_BINS]; -// final long transversionByQuality[] = new long[NUM_BINS]; -// final double titvByQuality[] = new double[NUM_BINS]; // the final ti/tv sets that get reported out -// -// public Object[] getRowKeys() { -// return new String[]{"sample"}; -// } -// -// public Object[] getColumnKeys() { -// final String columnKeys[] = new String[NUM_BINS]; -// for( int iii = 0; iii < NUM_BINS; iii++ ) { -// columnKeys[iii] = "titvBin" + iii; -// } -// return columnKeys; -// } -// -// public String getCell(int x, int y) { -// return String.valueOf(titvByQuality[y]); -// } -// -// public String toString() { -// StringBuffer returnString = new StringBuffer(); -// // output the ti/tv array -// returnString.append("titvByQuality: "); -// for( int iii = 0; iii < NUM_BINS; iii++ ) { -// returnString.append(titvByQuality[iii]); -// returnString.append(" "); -// } -// return returnString.toString(); -// } -// -// public void incrValue( final double qual, final boolean isTransition ) { -// final Integer qualKey = Math.round((float) qual); -// final long numTransition = (isTransition ? 1L : 0L); -// final long numTransversion = (isTransition ? 0L : 1L); -// if( qualByIsTransition.containsKey(qualKey) ) { -// Pair transitionPair = qualByIsTransition.get(qualKey); -// transitionPair.set(transitionPair.getFirst() + numTransition, transitionPair.getSecond() + numTransversion); -// qualByIsTransition.put(qualKey, transitionPair); -// } else { -// qualByIsTransition.put(qualKey, new Pair(numTransition,numTransversion)); -// } -// } -// -// public void organizeTiTvTables() { -// for( int iii = 0; iii < NUM_BINS; iii++ ) { -// transitionByQuality[iii] = 0L; -// transversionByQuality[iii] = 0L; -// titvByQuality[iii] = 0.0; -// } -// -// int maxQual = 0; -// -// // Calculate the maximum quality score in order to normalize and histogram -// for( final Integer qual : qualByIsTransition.keySet() ) { -// if( qual > maxQual ) { -// maxQual = qual; -// } -// } -// -// final double binSize = ((double)maxQual) / ((double) (NUM_BINS-1)); -// -// for( final Integer qual : qualByIsTransition.keySet() ) { -// final int index = (int)Math.floor( ((double) qual) / binSize ); -// if( index >= 0 ) { // BUGBUG: why is there overflow here? -// Pair transitionPair = qualByIsTransition.get(qual); -// transitionByQuality[index] += transitionPair.getFirst(); -// transversionByQuality[index] += transitionPair.getSecond(); -// } -// } -// -// for( int iii = 0; iii < NUM_BINS; iii++ ) { -// if( transitionByQuality[iii] + transversionByQuality[iii] > 800L ) { // need to have a sufficient number of variants to get a useful Ti/Tv ratio -// titvByQuality[iii] = ((double) transitionByQuality[iii]) / ((double) transversionByQuality[iii]); -// } else { -// titvByQuality[iii] = 0.0; -// } -// } -// -// } -// } -// -// class AlleleCountStats extends TableType { -// final HashMap> qualityListMap = new HashMap>(); -// final HashMap qualityMap = new HashMap(); -// -// public Object[] getRowKeys() { -// final int NUM_BINS = qualityListMap.keySet().size(); -// final String rowKeys[] = new String[NUM_BINS]; -// int iii = 0; -// for( final Integer key : qualityListMap.keySet() ) { -// rowKeys[iii] = "AC" + key; -// iii++; -// } -// return rowKeys; -// -// } -// -// public Object[] getColumnKeys() { -// return new String[]{"alleleCount","avgQual"}; -// } -// -// public String getCell(int x, int y) { -// int iii = 0; -// for( final Integer key : qualityListMap.keySet() ) { -// if(iii == x) { -// if(y == 0) { return String.valueOf(key); } -// else { return String.valueOf(qualityMap.get(key)); } -// } -// iii++; -// } -// return null; -// } -// -// public String toString() { -// String returnString = ""; -// // output the quality map -// returnString += "AlleleCountStats: "; -// //for( int iii = 0; iii < NUM_BINS; iii++ ) { -// // returnString += titvByQuality[iii] + " "; -// //} -// return returnString; -// } -// -// public void incrValue( final double qual, final int alleleCount ) { -// ArrayList list = qualityListMap.get(alleleCount); -// if(list==null) { list = new ArrayList(); } -// list.add(qual); -// qualityListMap.put(alleleCount, list); -// } -// -// public void organizeAlleleCountTables() { -// for( final Integer key : qualityListMap.keySet() ) { -// final ArrayList list = qualityListMap.get(key); -// double meanQual = 0.0; -// final double numQuals = (double)list.size(); -// for( Double qual : list ) { -// meanQual += qual / numQuals; -// } -// qualityMap.put(key, meanQual); -// } -// } -// } -// -// //public VariantQualityScore(VariantEvalWalker parent) { -// //super(parent); -// //} -// -// public String getName() { -// return "VariantQualityScore"; -// } -// -// public int getComparisonOrder() { -// return 1; // we only need to see each eval track -// } -// -// public String toString() { -// return getName(); -// } -// -// public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { -// final String interesting = null; -// -// if( eval != null && eval.isSNP() && eval.isBiallelic() && eval.isPolymorphicInSamples() ) { //BUGBUG: only counting biallelic sites (revisit what to do with triallelic sites) -// if( titvStats == null ) { titvStats = new TiTvStats(); } -// titvStats.incrValue(eval.getPhredScaledQual(), VariantContextUtils.isTransition(eval)); -// -// if( alleleCountStats == null ) { alleleCountStats = new AlleleCountStats(); } -// int alternateAlleleCount = 0; -// for (final Allele a : eval.getAlternateAlleles()) { -// alternateAlleleCount += eval.getCalledChrCount(a); -// } -// alleleCountStats.incrValue(eval.getPhredScaledQual(), alternateAlleleCount); -// } -// -// return interesting; // This module doesn't capture any interesting sites, so return null -// } -// -// public void finalizeEvaluation() { -// if( titvStats != null ) { -// titvStats.organizeTiTvTables(); -// } -// if( alleleCountStats != null ) { -// alleleCountStats.organizeAlleleCountTables(); -// } -// } -} \ No newline at end of file