Initial checkin of the ValidationGenotyper. Not intended to be used by anybody yet. Only here for archival purposes at this point.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4685 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin
parent
ef2f6d90d2
commit
b677080858
|
|
@ -0,0 +1,225 @@
|
|||
/*
|
||||
* 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.playground.gatk.walkers.validationgenotyper;
|
||||
|
||||
import org.broad.tribble.util.variantcontext.VariantContext;
|
||||
import org.broadinstitute.sting.commandline.Output;
|
||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
import org.broadinstitute.sting.gatk.walkers.*;
|
||||
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
|
||||
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
|
||||
import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
|
||||
import org.broadinstitute.sting.utils.SampleUtils;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
|
||||
import java.io.PrintStream;
|
||||
import java.util.ArrayList;
|
||||
import java.util.TreeSet;
|
||||
|
||||
/**
|
||||
* This is the validation genotyper. It is not ready to be used by anybody.
|
||||
*
|
||||
* @author rpoplin
|
||||
* @since Oct 20, 2010
|
||||
* @help.summary This is the validation genotyper. It is not ready to be used by anybody.
|
||||
*/
|
||||
|
||||
@Allows(value={DataSource.READS, DataSource.REFERENCE})
|
||||
public class ValidationGenotyper extends LocusWalker<ValidationGenotyper.CountedData, ValidationGenotyper.CountedData> implements TreeReducible<ValidationGenotyper.CountedData> {
|
||||
|
||||
@Output( doc="The output filtered VCF file", required=true)
|
||||
private PrintStream printStream = null;
|
||||
|
||||
public static class CountedData {
|
||||
private long numTP = 0L;
|
||||
private long numTN = 0L;
|
||||
private long numFP = 0L;
|
||||
private long numFilteringFN = 0L;
|
||||
private long numCallingFN = 0L;
|
||||
|
||||
/**
|
||||
* Adds the values of other to this, returning this
|
||||
* @param other the other object
|
||||
*/
|
||||
public void add(CountedData other) {
|
||||
numTP += other.numTP;
|
||||
numTN += other.numTN;
|
||||
numFP += other.numFP;
|
||||
numFilteringFN += other.numFilteringFN;
|
||||
numCallingFN += other.numCallingFN;
|
||||
}
|
||||
}
|
||||
|
||||
public enum VARIANT_STATUS {
|
||||
CALLED,
|
||||
FILTERED,
|
||||
MISSING
|
||||
}
|
||||
|
||||
final private ArrayList<String> evalNames = new ArrayList<String>();
|
||||
final private ArrayList<String> compNames = new ArrayList<String>();
|
||||
final private TreeSet<String> overlappingSamples = new TreeSet<String>();
|
||||
private UnifiedGenotyperEngine engine;
|
||||
|
||||
//---------------------------------------------------------------------------------------------------------------
|
||||
//
|
||||
// initialize
|
||||
//
|
||||
//---------------------------------------------------------------------------------------------------------------
|
||||
|
||||
public void initialize() {
|
||||
|
||||
for( ReferenceOrderedDataSource d : this.getToolkit().getRodDataSources() ) {
|
||||
if( d.getName().toLowerCase().startsWith("eval") ) {
|
||||
evalNames.add( d.getName() );
|
||||
} else if( d.getName().toLowerCase().startsWith("comp") ) {
|
||||
compNames.add( d.getName() );
|
||||
} else {
|
||||
throw new UserException.BadInput("Don't know what to do with input ROD track named: " + d.getName());
|
||||
}
|
||||
}
|
||||
|
||||
if( evalNames.size() != 1 || compNames.size() != 1 ) {
|
||||
throw new UserException.BadInput("Expecting to see exactly one eval track and exactly one comp track");
|
||||
}
|
||||
|
||||
final TreeSet<String> evalSamples = new TreeSet<String>();
|
||||
evalSamples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), evalNames));
|
||||
final TreeSet<String> compSamples = new TreeSet<String>();
|
||||
compSamples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), compNames));
|
||||
for( final String sample : evalSamples ) {
|
||||
if( compSamples.contains( sample ) ) {
|
||||
overlappingSamples.add( sample );
|
||||
}
|
||||
}
|
||||
|
||||
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
|
||||
uac.ALL_BASES_MODE = true;
|
||||
engine = new UnifiedGenotyperEngine(getToolkit(),uac);
|
||||
|
||||
logger.info( "Overlapping samples = " + overlappingSamples );
|
||||
}
|
||||
|
||||
//---------------------------------------------------------------------------------------------------------------
|
||||
//
|
||||
// map
|
||||
//
|
||||
//---------------------------------------------------------------------------------------------------------------
|
||||
|
||||
public CountedData map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
|
||||
|
||||
final CountedData counter = new CountedData();
|
||||
|
||||
if( tracker == null ) { // For some reason RodWalkers get map calls with null trackers
|
||||
return counter;
|
||||
}
|
||||
|
||||
VariantContext vcEval = tracker.getVariantContext(ref, evalNames.get(0), null, context.getLocation(), false);
|
||||
VariantContext vcComp = tracker.getVariantContext(ref, compNames.get(0), null, context.getLocation(), false);
|
||||
|
||||
if( vcEval != null ) { vcEval = vcEval.subContextFromGenotypes( vcEval.getGenotypes(overlappingSamples).values() ); }
|
||||
if( vcComp != null ) { vcComp = vcComp.subContextFromGenotypes( vcComp.getGenotypes(overlappingSamples).values() ); }
|
||||
|
||||
VARIANT_STATUS evalStatus;
|
||||
VARIANT_STATUS compStatus;
|
||||
|
||||
// First set the variant status variable for both the eval and comp then decide the site's T/F status
|
||||
if( vcEval != null && vcEval.isSNP() && vcEval.isPolymorphic() ) {
|
||||
if( !vcEval.isFiltered() ) {
|
||||
evalStatus = VARIANT_STATUS.CALLED;
|
||||
} else {
|
||||
evalStatus = VARIANT_STATUS.FILTERED;
|
||||
}
|
||||
} else {
|
||||
evalStatus = VARIANT_STATUS.MISSING;
|
||||
}
|
||||
if( vcComp != null && vcComp.isSNP() && vcComp.isPolymorphic() ) {
|
||||
if( !vcComp.isFiltered() ) {
|
||||
compStatus = VARIANT_STATUS.CALLED;
|
||||
} else {
|
||||
compStatus = VARIANT_STATUS.FILTERED;
|
||||
}
|
||||
} else {
|
||||
compStatus = VARIANT_STATUS.MISSING;
|
||||
}
|
||||
|
||||
if( evalStatus == VARIANT_STATUS.CALLED && compStatus == VARIANT_STATUS.CALLED ) { counter.numTP = 1L; }
|
||||
else if( evalStatus == VARIANT_STATUS.CALLED && compStatus == VARIANT_STATUS.FILTERED ) {
|
||||
counter.numFP = 1L;
|
||||
if( printStream!= null ) {
|
||||
printStream.println(vcEval.getChr() + ":" + vcEval.getStart() ); // Used to create interval lists of FP variants
|
||||
}
|
||||
}
|
||||
else if( evalStatus == VARIANT_STATUS.CALLED && compStatus == VARIANT_STATUS.MISSING ) {
|
||||
VariantCallContext call = engine.runGenotyper(tracker, ref, context);
|
||||
if( call != null && call.confidentlyCalled && call.vc != null && call.vc.getType() == VariantContext.Type.NO_VARIATION ) {
|
||||
counter.numFP = 1L;
|
||||
if( printStream!= null ) {
|
||||
printStream.println(vcEval.getChr() + ":" + vcEval.getStart() ); // Used to create interval lists of FP variants
|
||||
}
|
||||
}
|
||||
}
|
||||
else if( evalStatus == VARIANT_STATUS.FILTERED && compStatus == VARIANT_STATUS.CALLED ) { counter.numFilteringFN = 1L; }
|
||||
//if( evalStatus == VARIANT_STATUS.FILTERED && compStatus == VARIANT_STATUS.FILTERED ) { counter.numTP = 1L; }
|
||||
//if( evalStatus == VARIANT_STATUS.FILTERED && compStatus == VARIANT_STATUS.MISSING ) { counter.numTP = 1L; }
|
||||
else if( evalStatus == VARIANT_STATUS.MISSING && compStatus == VARIANT_STATUS.CALLED ) { counter.numCallingFN = 1L; }
|
||||
//if( evalStatus == VARIANT_STATUS.MISSING && compStatus == VARIANT_STATUS.FILTERED ) { counter.numTP = 1L; }
|
||||
//if( evalStatus == VARIANT_STATUS.MISSING && compStatus == VARIANT_STATUS.MISSING ) { counter.numTP = 1L; }
|
||||
return counter;
|
||||
}
|
||||
|
||||
//---------------------------------------------------------------------------------------------------------------
|
||||
//
|
||||
// reduce
|
||||
//
|
||||
//---------------------------------------------------------------------------------------------------------------
|
||||
|
||||
public CountedData reduceInit() {
|
||||
return new CountedData();
|
||||
}
|
||||
|
||||
public CountedData reduce( final CountedData mapValue, final CountedData reduceSum ) {
|
||||
reduceSum.add(mapValue);
|
||||
return reduceSum;
|
||||
}
|
||||
|
||||
public CountedData treeReduce( final CountedData sum1, final CountedData sum2) {
|
||||
sum2.add(sum1);
|
||||
return sum2;
|
||||
}
|
||||
|
||||
public void onTraversalDone( CountedData reduceSum ) {
|
||||
logger.info("TP = " + reduceSum.numTP);
|
||||
logger.info("TN = " + reduceSum.numTN);
|
||||
logger.info("FP = " + reduceSum.numFP);
|
||||
logger.info("FN = " + (reduceSum.numFilteringFN + reduceSum.numCallingFN) );
|
||||
logger.info(" filtering FN = " + reduceSum.numFilteringFN );
|
||||
logger.info(" calling FN = " + reduceSum.numCallingFN );
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue