zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

no longer useful 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4677 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-11-15 17:53:33 +00:00
parent 35382468ee
commit 62be55376b
1 changed files with 0 additions and 143 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

143
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TestVariantRecalibrator.java
View File

@ -1,143 +0,0 @@
/*
* 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.gatk.walkers.variantrecalibration;
import org.broad.tribble.dbsnp.DbSNPFeature;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.*;
import org.broadinstitute.sting.commandline.*;
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.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.text.XReadLines;
import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
import org.broadinstitute.sting.utils.collections.NestedHashMap;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.PrintStream;
import java.util.*;
/**
* Applies calibrated variant cluster parameters to variant calls to produce an accurate and informative variant quality score
*
* @author rpoplin
* @since Mar 17, 2010
*
* @help.summary Applies calibrated variant cluster parameters to variant calls to produce an accurate and informative variant quality score
*/
public class TestVariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDatum>, ExpandingArrayList<VariantDatum>> {
/////////////////////////////
// Inputs
/////////////////////////////
@Input(fullName="dataFile", shortName="dataFile", doc="The input cluster file generated by GenerateVariantClusters", required=true)
private File dataFile;
@Argument(fullName="target_titv", shortName="titv", doc="The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (~~2.07 for whole genome experiments)", required=true)
private double TARGET_TITV = 2.07;
@Argument(fullName="FDRtranche", shortName="tranche", doc="The levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)", required=false)
private double[] FDR_TRANCHES = null;
@Argument(fullName="maxElements", shortName="maxElements", doc="The expected novel Ti/Tv ratio to use when calculating FDR tranches and for display on optimization curve output figures. (~~2.07 for whole genome experiments)", required=false)
private double maxElements = -1;
@Argument(fullName="sixElementFile", shortName="sixElementFile", doc="", required=false)
private File sixElementFile = null;
@Argument(fullName="fourElementFile", shortName="fourElementFile", doc="", required=false)
private File fourElementFile = null;
public void initialize() {
List<VariantDatum> vd = new ArrayList<VariantDatum>();
try {
for ( String line : new XReadLines(dataFile, true) ) {
String[] parts = line.split(" ");
if ( ! parts[0].equals("QUAL") ) {
VariantDatum datum = new VariantDatum();
datum.qual = Double.valueOf(parts[0]);
datum.isTransition = parts[1].equals("1");
datum.isKnown = parts[2].equals("1");
vd.add(datum);
if ( maxElements != -1 && vd.size() > maxElements )
break;
}
}
} catch (FileNotFoundException e) {
throw new StingException("foo", e);
}
List<Tranche> tranches = VariantGaussianMixtureModel.findTranches(vd.toArray(new VariantDatum[0]), FDR_TRANCHES, TARGET_TITV);
System.out.printf(Tranche.tranchesString(tranches));
if ( sixElementFile != null ) {
List<Tranche> six = Tranche.readTraches(sixElementFile);
System.out.printf("six%n");
System.out.printf(Tranche.tranchesString(six));
}
if ( fourElementFile != null ) {
List<Tranche> four = Tranche.readTraches(fourElementFile);
System.out.printf("four%n");
System.out.printf(Tranche.tranchesString(four));
}
System.exit(0);
}
public ExpandingArrayList<VariantDatum> map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
return null;
}
//---------------------------------------------------------------------------------------------------------------
//
// reduce
//
//---------------------------------------------------------------------------------------------------------------
public ExpandingArrayList<VariantDatum> reduceInit() {
return new ExpandingArrayList<VariantDatum>();
}
public ExpandingArrayList<VariantDatum> reduce( final ExpandingArrayList<VariantDatum> mapValue, final ExpandingArrayList<VariantDatum> reduceSum ) {
reduceSum.addAll( mapValue );
return reduceSum;
}
public void onTraversalDone( ExpandingArrayList<VariantDatum> reduceSum ) {
}
}