Variant Eval module that collects indel statistics (basic counts and event sizes) and partitions by AC (similar to SimpleMetricsByAC in the SNP case)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4973 348d0f76-0448-11de-a6fe-93d51630548a
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delangel
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package org.broadinstitute.sting.gatk.walkers.varianteval;
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import org.broad.tribble.util.variantcontext.VariantContext;
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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.contexts.variantcontext.VariantContextUtils;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.utils.report.tags.Analysis;
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import org.broadinstitute.sting.utils.report.tags.DataPoint;
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import org.broadinstitute.sting.utils.report.utils.TableType;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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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 delangel
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* @since Apr 11, 2010
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*/
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@Analysis(name = "Indel Metrics by allele count", description = "Shows various stats binned by allele count")
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public class IndelMetricsByAC extends VariantEvaluator implements StandardEval {
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// a mapping from quality score histogram bin to Ti/Tv ratio
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@DataPoint(name="Indel Metrics by AC", description = "Indel Metrics by allele count")
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MetricsByAc metrics = null;
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//@DataPoint(name="Quality by Allele Count", description = "average variant quality for each allele count")
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//AlleleCountStats alleleCountStats = null;
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private static final int INDEL_SIZE_LIMIT = 100;
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private static final int NUM_SCALAR_COLUMNS = 6;
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static int len2Index(int ind) {
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return ind+INDEL_SIZE_LIMIT+NUM_SCALAR_COLUMNS;
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}
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static int index2len(int ind) {
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return ind-INDEL_SIZE_LIMIT-NUM_SCALAR_COLUMNS;
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}
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protected final static String[] METRIC_COLUMNS;
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static {
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METRIC_COLUMNS= new String[NUM_SCALAR_COLUMNS+2*INDEL_SIZE_LIMIT+1];
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METRIC_COLUMNS[0] = "AC";
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METRIC_COLUMNS[1] = "nIns";
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METRIC_COLUMNS[2] = "nDels";
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METRIC_COLUMNS[3] = "n";
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METRIC_COLUMNS[4] = "nComplex";
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METRIC_COLUMNS[5] = "nLong";
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for (int k=NUM_SCALAR_COLUMNS; k < NUM_SCALAR_COLUMNS+ 2*INDEL_SIZE_LIMIT+1; k++)
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METRIC_COLUMNS[k] = "indel_size_len"+Integer.valueOf(index2len(k));
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}
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class MetricsAtAC {
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public int ac = -1, nIns =0, nDel = 0, nComplex = 0, nLong;
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public int sizeCount[] = new int[2*INDEL_SIZE_LIMIT+1];
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public MetricsAtAC(int ac) { this.ac = ac; }
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public void update(VariantContext eval) {
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int eventLength = 0;
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if ( eval.isInsertion() ) {
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eventLength = eval.getAlternateAllele(0).length();
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nIns++;
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} else if ( eval.isDeletion() ) {
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eventLength = -eval.getReference().length();
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nDel++;
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}
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else {
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nComplex++;
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}
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if (Math.abs(eventLength) < INDEL_SIZE_LIMIT)
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sizeCount[len2Index(eventLength)]++;
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else
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nLong++;
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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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if (i >= NUM_SCALAR_COLUMNS && i <=NUM_SCALAR_COLUMNS+ 2*INDEL_SIZE_LIMIT)
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return String.valueOf(sizeCount[i-NUM_SCALAR_COLUMNS]);
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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(nIns);
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case 2: return String.valueOf(nDel);
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case 3: return String.valueOf(nIns + nDel);
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case 4: return String.valueOf(nComplex);
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case 5: return String.valueOf(nLong);
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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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//
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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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String returnString = "";
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return returnString;
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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.getChromosomeCount(eval.getAlternateAllele(0));
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else if ( eval.hasAttribute("AC") ) {
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ac = Integer.valueOf(eval.getAttributeAsString("AC"));
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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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public IndelMetricsByAC(VariantEvalWalker parent) {
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super(parent);
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// don't do anything
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}
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public String getName() {
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return "IndelMetricsByAC";
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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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final String interesting = null;
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if (eval != null ) {
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if ( metrics == null ) {
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int nSamples = this.getVEWalker().getNSamplesForEval(eval);
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if ( nSamples != -1 )
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metrics = new MetricsByAc(2 * nSamples);
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}
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if ( eval.isIndel() && eval.isBiallelic() &&
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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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//public void finalizeEvaluation() {
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//
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//}
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}
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