Initial version of Indel Statistics module for Variant Eval - not for general use yet, needs more verification and more work. Older IndelHistogram module will be obsolete with this new walker. Right now, for each sample (and for all samples), the following are computed:
- Number of insertions - Number of deletions - Length distribution for indels. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4694 348d0f76-0448-11de-a6fe-93d51630548a
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package org.broadinstitute.sting.gatk.walkers.varianteval;
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import org.broad.tribble.util.variantcontext.Genotype;
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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.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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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 java.util.HashMap;
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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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@Analysis(name = "Indel Statistics", description = "Shows various indel metrics and statistics")
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public class IndelStatistics extends VariantEvaluator {
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@DataPoint(name="IndelStatistics", description = "Indel Statistics")
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IndelStats indelStats = null;
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private static final int INDEL_SIZE_LIMIT = 100;
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private static final int NUM_SCALAR_COLUMNS = 8;
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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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static class IndelStats implements TableType {
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protected final static String ALL_SAMPLES_KEY = "allSamples";
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protected final static String[] COLUMN_KEYS;
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static {
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COLUMN_KEYS= new String[NUM_SCALAR_COLUMNS+2*INDEL_SIZE_LIMIT+1];
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COLUMN_KEYS[0] = "heterozygosity";
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COLUMN_KEYS[1] = "number_of_insertions";
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COLUMN_KEYS[2] = "number_of_deletions";
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COLUMN_KEYS[3] = "number_het_insertions";
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COLUMN_KEYS[4] = "number_homozygous_insertions";
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COLUMN_KEYS[5] = "number_het_deletions";
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COLUMN_KEYS[6] = "number_homozygous_deletions";
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COLUMN_KEYS[7] = "number of homozygous reference sites";
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for (int k=NUM_SCALAR_COLUMNS; k < NUM_SCALAR_COLUMNS+ 2*INDEL_SIZE_LIMIT+1; k++)
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COLUMN_KEYS[k] = "indel_size_len"+Integer.valueOf(index2len(k));
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}
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// map of sample to statistics
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protected final HashMap<String, double[]> indelSummary = new HashMap<String, double[]>();
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public IndelStats(final VariantContext vc) {
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indelSummary.put(ALL_SAMPLES_KEY, new double[COLUMN_KEYS.length]);
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for( final String sample : vc.getGenotypes().keySet() ) {
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indelSummary.put(sample, new double[COLUMN_KEYS.length]);
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}
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}
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/**
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*
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* @return one row per sample
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*/
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public Object[] getRowKeys() {
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return indelSummary.keySet().toArray(new String[indelSummary.size()]);
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}
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public Object getCell(int x, int y) {
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final Object[] rowKeys = getRowKeys();
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return String.format("%4.2f",indelSummary.get(rowKeys[x])[y]);
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}
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/**
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* get the column keys
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* @return a list of objects, in this case strings, that are the column names
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*/
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public Object[] getColumnKeys() {
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return COLUMN_KEYS;
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}
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public String getName() {
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return "IndelStats";
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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 String toString() {
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return getName();
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}
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/*
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private double ratio(long numer, long denom) {
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return denom != 0L ? 100.0 * ( ((double)numer) / ((double)denom) ) : 0.0;
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}
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final long[] allSamplesNumerators = new long[COLUMN_KEYS.length];
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final long[] allSamplesDenominators = new long[COLUMN_KEYS.length];
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private void updateSummaries(int i, double[] summary, long numer, long denom ) {
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allSamplesNumerators[i] += numer;
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allSamplesDenominators[i] += denom;
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summary[i] = ratio(numer, denom);
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}
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*/
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/*
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* increment the specified value
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*/
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public void incrValue(VariantContext vc) {
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int eventLength = 0;
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boolean isInsertion = false;
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if ( vc.isInsertion() ) {
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eventLength = vc.getAlternateAllele(0).length();
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indelSummary.get(ALL_SAMPLES_KEY)[1]++;
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isInsertion = true;
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} else if ( vc.isDeletion() ) {
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indelSummary.get(ALL_SAMPLES_KEY)[2]++;
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eventLength = -vc.getReference().length();
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}
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indelSummary.get(ALL_SAMPLES_KEY)[len2Index(eventLength)]++;
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for( final String sample : vc.getGenotypes().keySet() ) {
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if ( indelSummary.containsKey(sample) ) {
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Genotype g = vc.getGenotype(sample);
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boolean isVariant = (g.isCalled() && !g.isHomRef());
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if (isVariant) {
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// update ins/del count
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if (isInsertion) {
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indelSummary.get(sample)[1]++;
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}
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else
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indelSummary.get(sample)[2]++;
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// update histogram
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indelSummary.get(sample)[len2Index(eventLength)]++;
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if (g.isHet())
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if (isInsertion)
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indelSummary.get(sample)[3]++;
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else
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indelSummary.get(sample)[5]++;
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else
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if (isInsertion)
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indelSummary.get(sample)[4]++;
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else
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indelSummary.get(sample)[6]++;
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}
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else
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indelSummary.get(sample)[7]++;
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}
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}
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}
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}
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public IndelStatistics(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 "IndelStatistics";
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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 update2(VariantContext eval, VariantContext validation, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context, VariantEvalWalker.EvaluationContext group) {
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return null;
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}
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public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if (eval != null ) {
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if ( indelStats == null ) {
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int nSamples = this.getVEWalker().getNSamplesForEval(eval);
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if ( nSamples != -1 )
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indelStats = new IndelStats(eval);
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}
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if ( eval.isIndel() &&
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eval.isBiallelic() &&
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indelStats != null ) {
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indelStats.incrValue(eval);
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}
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}
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return null; // This module doesn't capture any interesting sites, so return null
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}
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public String update0(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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return null;
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}
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public void finalizeEvaluation() {
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//
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int k=0;
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}
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}
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