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TrainingSets class is obsolete now.

This commit is contained in:
Ryan Poplin 2011-08-10 10:23:33 -04:00
parent 60639e5aa5
commit bc125f104a
2 changed files with 0 additions and 73 deletions
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71
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
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@ -1,71 +0,0 @@
/*
* Copyright (c) 2011 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.apache.log4j.Logger;
import org.broadinstitute.sting.commandline.Tags;
/**
* Created by IntelliJ IDEA.
* User: rpoplin
* Date: 3/12/11
*/
public class TrainingSet {
public String name;
public boolean isKnown = false;
public boolean isTraining = false;
public boolean isAntiTraining = false;
public boolean isTruth = false;
public boolean isConsensus = false;
public double prior = 0.0;
protected final static Logger logger = Logger.getLogger(TrainingSet.class);
public TrainingSet( final String name, final Tags tags ) {
this.name = name;
// Parse the tags to decide which tracks have which properties
if( tags != null ) {
isKnown = tags.containsKey("known") && tags.getValue("known").equals("true");
isTraining = tags.containsKey("training") && tags.getValue("training").equals("true");
isAntiTraining = tags.containsKey("bad") && tags.getValue("bad").equals("true");
isTruth = tags.containsKey("truth") && tags.getValue("truth").equals("true");
isConsensus = tags.containsKey("consensus") && tags.getValue("consensus").equals("true");
prior = ( tags.containsKey("prior") ? Double.parseDouble(tags.getValue("prior")) : prior );
}
// Report back to the user which tracks were found and the properties that were detected
if( !isConsensus && !isAntiTraining ) {
logger.info( String.format( "Found %s track: \tKnown = %s \tTraining = %s \tTruth = %s \tPrior = Q%.1f", this.name, isKnown, isTraining, isTruth, prior) );
} else if( isConsensus ) {
logger.info( String.format( "Found consensus track: %s", this.name) );
} else {
logger.info( String.format( "Found bad sites training track: %s", this.name) );
}
}
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -52,7 +52,6 @@ public class VariantDataManager {
private final double[] meanVector;
private final double[] varianceVector; // this is really the standard deviation
public final ArrayList<String> annotationKeys;
private final ExpandingArrayList<TrainingSet> trainingSets;
private final VariantRecalibratorArgumentCollection VRAC;
protected final static Logger logger = Logger.getLogger(VariantDataManager.class);
@ -63,7 +62,6 @@ public class VariantDataManager {
this.VRAC = VRAC;
meanVector = new double[this.annotationKeys.size()];
varianceVector = new double[this.annotationKeys.size()];
trainingSets = new ExpandingArrayList<TrainingSet>();
}
public void setData( final ExpandingArrayList<VariantDatum> data ) {