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Obsolete covariate class 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5993 348d0f76-0448-11de-a6fe-93d51630548a
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ebanks 2011-06-14 14:11:47 +00:00
parent 11eb74e44f
commit d00d4fd4d6
1 changed files with 0 additions and 69 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java
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/*
* The MIT License
*
* Copyright (c) 2009 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.recalibration;
import net.sf.samtools.SAMRecord;
import net.sf.picard.util.IlluminaUtil;
import org.broadinstitute.sting.utils.exceptions.UserException;
/**
* @author alecw@broadinstitute.org
*/
public class TileCovariate implements ExperimentalCovariate {
private boolean exceptionWhenNoTile = false;
// Initialize any member variables using the command-line arguments passed to the walkers
public void initialize( final RecalibrationArgumentCollection RAC ) {
exceptionWhenNoTile = RAC.EXCEPTION_IF_NO_TILE;
}
// Used to pick out the covariate's value from attributes of the read
public Comparable getValue(final SAMRecord read, final int offset) {
Integer tile = IlluminaUtil.getTileFromReadName(read.getReadName());
if (tile == null) {
if( exceptionWhenNoTile ) {
throw new UserException.MalformedBAM(read, "Tile covariate specified but tile number not defined for read: " + read.getReadName() );
} else {
return -1;
}
}
return tile;
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
public Comparable getValue(final String str) {
return Integer.parseInt( str );
}
public void getValues(SAMRecord read, Comparable[] comparable) {
final Comparable tileCovariateValue = getValue(read, 0);
for(int i = 0; i < read.getReadLength(); i++) {
comparable[i] = tileCovariateValue;
}
}
}