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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 2011-01-12 01:08:09 +00:00
parent 48052907a6
commit 23597a2bde
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java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelMetricsByAC.java 100755
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package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.util.ArrayList;
/*
* 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.
*/
/**
* @author delangel
* @since Apr 11, 2010
*/
@Analysis(name = "Indel Metrics by allele count", description = "Shows various stats binned by allele count")
public class IndelMetricsByAC extends VariantEvaluator implements StandardEval {
// a mapping from quality score histogram bin to Ti/Tv ratio
@DataPoint(name="Indel Metrics by AC", description = "Indel Metrics by allele count")
MetricsByAc metrics = null;
//@DataPoint(name="Quality by Allele Count", description = "average variant quality for each allele count")
//AlleleCountStats alleleCountStats = null;
private static final int INDEL_SIZE_LIMIT = 100;
private static final int NUM_SCALAR_COLUMNS = 6;
static int len2Index(int ind) {
return ind+INDEL_SIZE_LIMIT+NUM_SCALAR_COLUMNS;
}
static int index2len(int ind) {
return ind-INDEL_SIZE_LIMIT-NUM_SCALAR_COLUMNS;
}
protected final static String[] METRIC_COLUMNS;
static {
METRIC_COLUMNS= new String[NUM_SCALAR_COLUMNS+2*INDEL_SIZE_LIMIT+1];
METRIC_COLUMNS[0] = "AC";
METRIC_COLUMNS[1] = "nIns";
METRIC_COLUMNS[2] = "nDels";
METRIC_COLUMNS[3] = "n";
METRIC_COLUMNS[4] = "nComplex";
METRIC_COLUMNS[5] = "nLong";
for (int k=NUM_SCALAR_COLUMNS; k < NUM_SCALAR_COLUMNS+ 2*INDEL_SIZE_LIMIT+1; k++)
METRIC_COLUMNS[k] = "indel_size_len"+Integer.valueOf(index2len(k));
}
class MetricsAtAC {
public int ac = -1, nIns =0, nDel = 0, nComplex = 0, nLong;
public int sizeCount[] = new int[2*INDEL_SIZE_LIMIT+1];
public MetricsAtAC(int ac) { this.ac = ac; }
public void update(VariantContext eval) {
int eventLength = 0;
if ( eval.isInsertion() ) {
eventLength = eval.getAlternateAllele(0).length();
nIns++;
} else if ( eval.isDeletion() ) {
eventLength = -eval.getReference().length();
nDel++;
}
else {
nComplex++;
}
if (Math.abs(eventLength) < INDEL_SIZE_LIMIT)
sizeCount[len2Index(eventLength)]++;
else
nLong++;
}
// corresponding to METRIC_COLUMNS
public String getColumn(int i) {
if (i >= NUM_SCALAR_COLUMNS && i <=NUM_SCALAR_COLUMNS+ 2*INDEL_SIZE_LIMIT)
return String.valueOf(sizeCount[i-NUM_SCALAR_COLUMNS]);
switch (i) {
case 0: return String.valueOf(ac);
case 1: return String.valueOf(nIns);
case 2: return String.valueOf(nDel);
case 3: return String.valueOf(nIns + nDel);
case 4: return String.valueOf(nComplex);
case 5: return String.valueOf(nLong);
default:
throw new ReviewedStingException("Unexpected column " + i);
}
}
}
class MetricsByAc implements TableType {
ArrayList<MetricsAtAC> metrics = new ArrayList<MetricsAtAC>();
Object[] rows = null;
public MetricsByAc( int nchromosomes ) {
rows = new Object[nchromosomes+1];
metrics = new ArrayList<MetricsAtAC>(nchromosomes+1);
for ( int i = 0; i < nchromosomes + 1; i++ ) {
metrics.add(new MetricsAtAC(i));
rows[i] = "ac" + i;
}
}
public Object[] getRowKeys() {
return rows;
}
public Object[] getColumnKeys() {
return METRIC_COLUMNS;
}
public String getName() {
return "MetricsByAc";
}
//
public String getCell(int ac, int y) {
return metrics.get(ac).getColumn(y);
}
public String toString() {
String returnString = "";
return returnString;
}
public void incrValue( VariantContext eval ) {
int ac = -1;
if ( eval.hasGenotypes() )
ac = eval.getChromosomeCount(eval.getAlternateAllele(0));
else if ( eval.hasAttribute("AC") ) {
ac = Integer.valueOf(eval.getAttributeAsString("AC"));
}
if ( ac != -1 )
metrics.get(ac).update(eval);
}
}
public IndelMetricsByAC(VariantEvalWalker parent) {
super(parent);
// don't do anything
}
public String getName() {
return "IndelMetricsByAC";
}
public int getComparisonOrder() {
return 1; // we only need to see each eval track
}
public boolean enabled() {
return true;
}
public String toString() {
return getName();
}
public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
final String interesting = null;
if (eval != null ) {
if ( metrics == null ) {
int nSamples = this.getVEWalker().getNSamplesForEval(eval);
if ( nSamples != -1 )
metrics = new MetricsByAc(2 * nSamples);
}
if ( eval.isIndel() && eval.isBiallelic() &&
metrics != null ) {
metrics.incrValue(eval);
}
}
return interesting; // This module doesn't capture any interesting sites, so return null
}
//public void finalizeEvaluation() {
//
//}
}