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Add tile to ReadHashDatum, and implement TileCovariate 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2166 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
alecw 2009-11-25 21:41:42 +00:00
parent db40e28e54
commit ac1b289d55
4 changed files with 61 additions and 5 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
View File

@ -18,6 +18,7 @@ import java.util.*;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord;
import edu.mit.broad.picard.illumina.parser.IlluminaUtil;
/*
* Copyright (c) 2009 The Broad Institute
@ -237,7 +238,8 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
logger.info( "The covariates being used here: " );
logger.info( requestedCovariates );
if(estimatedCapacity > 300 * 40 * 200 * 16) { estimatedCapacity = 300 * 40 * 200 * 16; } // Don't want to crash with out of heap space exception
if(estimatedCapacity > 300 * 40 * 200 * 16 || estimatedCapacity < 0) // could be negative if overflowed
{ estimatedCapacity = 300 * 40 * 200 * 16; } // Don't want to crash with out of heap space exception
dataManager = new RecalDataManager( estimatedCapacity );
readDatumHashMap = new IdentityHashMap<SAMRecord, ReadHashDatum>();
}
@ -347,8 +349,8 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
if( FORCE_PLATFORM != null ) {
platform = FORCE_PLATFORM;
}
readDatum = new ReadHashDatum( readGroupId, platform, quals, bases, isNegStrand, mappingQuality, length );
Integer tile = IlluminaUtil.getTileFromReadName(read.getReadName());
readDatum = new ReadHashDatum( readGroupId, platform, quals, bases, isNegStrand, mappingQuality, length, tile );
readDatumHashMap.put( read, readDatum );
sizeOfReadDatumHashMap++;
}

6
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadHashDatum.java
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@ -13,8 +13,10 @@ public class ReadHashDatum {
public boolean isNegStrand;
public int mappingQuality;
public int length;
public Integer tile;
public ReadHashDatum(String _readGroup, String _platform, byte[] _quals, byte[] _bases, boolean _isNegStrand, int _mappingQuality, int _length) {
public ReadHashDatum(String _readGroup, String _platform, byte[] _quals, byte[] _bases, boolean _isNegStrand,
int _mappingQuality, int _length, Integer _tile) {
readGroup = _readGroup;
platform = _platform;
quals = _quals;
@ -22,6 +24,7 @@ public class ReadHashDatum {
isNegStrand = _isNegStrand;
mappingQuality = _mappingQuality;
length = _length;
tile = _tile;
}
public ReadHashDatum(ReadHashDatum that) {
@ -32,5 +35,6 @@ public class ReadHashDatum {
this.isNegStrand = that.isNegStrand;
this.mappingQuality = that.mappingQuality;
this.length = that.length;
this.tile = that.tile;
}
}

6
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
View File

@ -15,6 +15,8 @@ import java.util.regex.Pattern;
import java.io.File;
import java.io.FileNotFoundException;
import edu.mit.broad.picard.illumina.parser.IlluminaUtil;
/*
* Copyright (c) 2009 The Broad Institute
*
@ -332,7 +334,9 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
platform = FORCE_PLATFORM;
}
ReadHashDatum readDatum = new ReadHashDatum( readGroupId, platform, originalQuals, bases, isNegStrand, read.getMappingQuality(), bases.length );
Integer tile = IlluminaUtil.getTileFromReadName(read.getReadName());
ReadHashDatum readDatum = new ReadHashDatum( readGroupId, platform, originalQuals, bases, isNegStrand,
read.getMappingQuality(), bases.length, tile );
// For each base in the read
for( int iii = startPos; iii < stopPos; iii++ ) { // Skip first or last base because there is no dinuc depending on the direction of the read

46
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java 100644
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@ -0,0 +1,46 @@
/*
* 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 org.broadinstitute.sting.utils.StingException;
/**
* @author alecw@broadinstitute.org
*/
public class TileCovariate implements Covariate {
public Comparable getValue(final ReadHashDatum readDatum, final int offset) {
if (readDatum.tile == null) {
throw new StingException("Tile number not defined for read");
}
return readDatum.tile;
}
public Comparable getValue(final String str) {
return Integer.parseInt( str );
}
public int estimatedNumberOfBins() {
return 120;
}
}