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Ti/Tv by AC 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3252 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-04-23 17:56:29 +00:00
parent 42bcca1010
commit 7f4d5d9973
3 changed files with 169 additions and 7 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
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@ -57,7 +57,7 @@ public class GenotypeConcordance extends VariantEvaluator {
@DataPoint(description = "the variant quality score histograms for true positive and false positive calls")
QualityScoreHistograms qualityScoreHistograms = null;
private static final int MAX_MISSED_VALIDATION_DATA = 10000;
private static final int MAX_MISSED_VALIDATION_DATA = 100;
class FrequencyStats implements TableType {

161
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java 100755
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@ -0,0 +1,161 @@
package org.broadinstitute.sting.gatk.walkers.varianteval;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.StingException;
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 depristo
* @since Apr 11, 2010
*/
@Analysis(name = "Quality Metrics by allele count", description = "Shows various stats binned by allele count")
public class SimpleMetricsByAC extends VariantEvaluator {
// a mapping from quality score histogram bin to Ti/Tv ratio
@DataPoint(name="TiTv by AC", description = "TiTv by allele count")
MetricsByAc metrics = null;
//@DataPoint(name="Quality by Allele Count", description = "average variant quality for each allele count")
//AlleleCountStats alleleCountStats = null;
private final static Object[] METRIC_COLUMNS = {"AC", "nTi", "nTv", "n", "Ti/Tv"};
class MetricsAtAC {
public int ac = -1, nTi = 0, nTv = 0;
public MetricsAtAC(int ac) { this.ac = ac; }
public void update(VariantContext eval) {
if ( eval.isTransition() )
nTi++;
else
nTv++;
}
// corresponding to METRIC_COLUMNS
public String getColumn(int i) {
switch (i) {
case 0: return String.valueOf(ac);
case 1: return String.valueOf(nTi);
case 2: return String.valueOf(nTv);
case 3: return String.valueOf(nTi + nTv);
case 4: return String.valueOf(ratio(nTi, nTv));
default:
throw new StingException("Unexpected column " + i);
}
}
}
class MetricsByAc implements TableType {
int nchromosomes = -1;
ArrayList<MetricsAtAC> metrics = new ArrayList<MetricsAtAC>();
Object[] rows = null;
public MetricsByAc( int nchromosomes ) {
this.nchromosomes = 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 an = eval.getChromosomeCount();
if ( an == nchromosomes ) { // ignore sites with no calls
int ac = eval.getChromosomeCount(eval.getAlternateAllele(0));
metrics.get(ac).update(eval);
}
}
}
public SimpleMetricsByAC(VariantEvalWalker parent) {
// don't do anything
}
public String getName() {
return "SimpleMetricsByAC";
}
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 && eval.isSNP() && eval.hasGenotypes() ) {
if ( metrics == null )
metrics = new MetricsByAc(2 * eval.getNSamples());
metrics.incrValue(eval);
}
return interesting; // This module doesn't capture any interesting sites, so return null
}
//public void finalizeEvaluation() {
//
//}
}

13
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
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@ -7,7 +7,8 @@ import java.util.Arrays;
import java.util.HashMap;
import java.util.Map;
public class VariantEvalIntegrationTest extends WalkerTest {
public class
VariantEvalIntegrationTest extends WalkerTest {
private static String cmdRoot = "-T VariantEval" +
" -R " + oneKGLocation + "reference/human_b36_both.fasta -reportType Grep";
@ -19,8 +20,8 @@ public class VariantEvalIntegrationTest extends WalkerTest {
@Test
public void testVESimple() {
HashMap<String, String> expectations = new HashMap<String, String>();
expectations.put("-L 1:1-10,000,000", "b28ffcff420177d9b73aa726e260fb34");
expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "749d53687497d7939713e9ce586642a4");
expectations.put("-L 1:1-10,000,000", "f2ce1e0e9bbe81b482a9448cb88e2263");
expectations.put("-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 0", "b39229f55b726c2f61a17463a3c883be");
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs = entry.getKey();
@ -41,10 +42,10 @@ public class VariantEvalIntegrationTest extends WalkerTest {
" -B comp_hapmap,VCF," + validationDataLocation + "CEU_hapmap_nogt_23.vcf";
String matchingMD5 = "3abf37ada16619f4b3f39cb7ecad497f";
String matchingMD5 = "f8c7bd3ce4499cff485d2170ce896af9";
expectations.put("", matchingMD5);
expectations.put(" -known comp_hapmap -known dbsnp", matchingMD5);
expectations.put(" -known comp_hapmap", "75026dbdad38f74ac697a7c102e64db4");
expectations.put(" -known comp_hapmap", "99c687b95b1a4614cd76570bfd24e7a6");
for ( Map.Entry<String, String> entry : expectations.entrySet() ) {
String extraArgs2 = entry.getKey();
@ -62,7 +63,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
String extraArgs = "-L 1:1-10,000,000 -family NA19238+NA19239=NA19240 -MVQ 30";
WalkerTestSpec spec = new WalkerTestSpec( root + " " + extraArgs + " -o %s -outputVCF %s",
2,
Arrays.asList("06cdbe7f94990dfe61b5e3ec03b49151", "b4a42c90318adc88361691ece50426f2"));
Arrays.asList("bfbad4053c89c264cec16040df0bcc4c", "b4a42c90318adc88361691ece50426f2"));
executeTest("testVEWriteVCF", spec);
}
}