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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Eric Banks 2012-02-06 11:53:31 -05:00
parent edb4edc08f 096c23a473
commit fbbd04621d
20 changed files with 131 additions and 132 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -215,8 +215,8 @@ public class GenomeAnalysisEngine {
resetRandomGenerator(System.currentTimeMillis());
// if the use specified an input BQSR recalibration table then enable on the fly recalibration
if (this.getArguments().RECAL_FILE != null)
setBaseRecalibration(this.getArguments().RECAL_FILE);
if (this.getArguments().BQSR_RECAL_FILE != null)
setBaseRecalibration(this.getArguments().BQSR_RECAL_FILE);
// Determine how the threads should be divided between CPU vs. IO.
determineThreadAllocation();

2
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -192,7 +192,7 @@ public class GATKArgumentCollection {
* and the raw empirical quality score calculated by phred-scaling the mismatch rate.
*/
@Input(fullName="BQSR", shortName="BQSR", required=false, doc="Filename for the input covariates table recalibration .csv file which enables on the fly base quality score recalibration")
public File RECAL_FILE = null; // BUGBUG: need a better argument name once we decide how BQSRs v1 and v2 will live in the code base simultaneously
public File BQSR_RECAL_FILE = null; // BUGBUG: need a better argument name once we decide how BQSRs v1 and v2 will live in the code base simultaneously
@Argument(fullName="defaultBaseQualities", shortName = "DBQ", doc = "If reads are missing some or all base quality scores, this value will be used for all base quality scores", required=false)
public byte defaultBaseQualities = -1;

9
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ContextCovariate.java
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@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.recalibration;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
import java.util.Arrays;
@ -35,19 +36,21 @@ import java.util.Arrays;
* Date: 9/26/11
*/
public class ContextCovariate implements Covariate {
public class ContextCovariate implements ExperimentalCovariate {
final int CONTEXT_SIZE = 8;
String allN = "";
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize( final RecalibrationArgumentCollection RAC ) {
for( int iii = 0; iii < CONTEXT_SIZE; iii++ ) {
allN += "N";
}
}
public void getValues(SAMRecord read, Comparable[] comparable) {
@Override
public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
byte[] bases = read.getReadBases();
for(int i = 0; i < read.getReadLength(); i++) {
comparable[i] = ( i-CONTEXT_SIZE < 0 ? allN : new String(Arrays.copyOfRange(bases,i-CONTEXT_SIZE,i)) );
@ -55,8 +58,8 @@ public class ContextCovariate implements Covariate {
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
@Override
public final Comparable getValue( final String str ) {
return str;
}
}

3
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
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@ -41,6 +41,7 @@ import org.broadinstitute.sting.utils.collections.NestedHashMap;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.PrintStream;
@ -374,7 +375,7 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
RecalDataManager.parseColorSpace( gatkRead );
gatkRead.setTemporaryAttribute( COVARS_ATTRIBUTE,
RecalDataManager.computeCovariates( gatkRead, requestedCovariates ));
RecalDataManager.computeCovariates( gatkRead, requestedCovariates, BaseRecalibration.BaseRecalibrationType.BASE_SUBSTITUTION ));
}
// Skip this position if base quality is zero

10
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.recalibration;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
/*
* Copyright (c) 2009 The Broad Institute
@ -32,7 +33,7 @@ import net.sf.samtools.SAMRecord;
* User: rpoplin
* Date: Oct 30, 2009
*
* The Covariate interface. A Covariate is a feature used in the recalibration that can be picked out of the read, offset, and corresponding reference bases
* The Covariate interface. A Covariate is a feature used in the recalibration that can be picked out of the read.
* In general most error checking and adjustments to the data are done before the call to the covariates getValue methods in order to speed up the code.
* This unfortunately muddies the code, but most of these corrections can be done per read while the covariates get called per base, resulting in a big speed up.
*/
@ -40,9 +41,10 @@ import net.sf.samtools.SAMRecord;
public interface Covariate {
public void initialize( RecalibrationArgumentCollection RAC ); // Initialize any member variables using the command-line arguments passed to the walkers
public Comparable getValue( String str ); // Used to get the covariate's value from input csv file in TableRecalibrationWalker
public void getValues( SAMRecord read, Comparable[] comparable ); //Takes an array of size (at least) read.getReadLength() and fills it with covariate
//values for each position in the read. This method was created as an optimization over calling getValue( read, offset ) for each offset and allows
//read-specific calculations to be done just once rather than for each offset.
public void getValues( SAMRecord read, Comparable[] comparable, BaseRecalibration.BaseRecalibrationType modelType );
//Takes an array of size (at least) read.getReadLength() and fills it with covariate
//values for each position in the read. This method was created as an optimization over calling getValue( read, offset ) for each offset and allows
//read-specific calculations to be done just once rather than for each offset.
}
interface RequiredCovariate extends Covariate {

6
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
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@ -4,6 +4,7 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.NGSPlatform;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.EnumSet;
@ -51,6 +52,7 @@ public class CycleCovariate implements StandardCovariate {
private final static EnumSet<NGSPlatform> FLOW_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.LS454, NGSPlatform.ION_TORRENT);
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize( final RecalibrationArgumentCollection RAC ) {
if( RAC.DEFAULT_PLATFORM != null ) {
if( RAC.DEFAULT_PLATFORM.equalsIgnoreCase( "SLX" ) || RAC.DEFAULT_PLATFORM.equalsIgnoreCase( "ILLUMINA" ) ||
@ -63,7 +65,8 @@ public class CycleCovariate implements StandardCovariate {
}
// Used to pick out the covariate's value from attributes of the read
public void getValues(SAMRecord read, Comparable[] comparable) {
@Override
public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
//-----------------------------
// Illumina, Solid, PacBio, and Complete Genomics
@ -164,6 +167,7 @@ public class CycleCovariate implements StandardCovariate {
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
@Override
public final Comparable getValue( final String str ) {
return Integer.parseInt( str );
}

50
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java
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@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
import java.util.HashMap;
@ -48,6 +49,7 @@ public class DinucCovariate implements StandardCovariate {
private HashMap<Integer, Dinuc> dinucHashMap;
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize( final RecalibrationArgumentCollection RAC ) {
final byte[] BASES = { (byte)'A', (byte)'C', (byte)'G', (byte)'T' };
dinucHashMap = new HashMap<Integer, Dinuc>();
@ -60,45 +62,11 @@ public class DinucCovariate implements StandardCovariate {
dinucHashMap.put( Dinuc.hashBytes(NO_CALL, NO_CALL), NO_DINUC );
}
/*
// Used to pick out the covariate's value from attributes of the read
public final Comparable getValue( final SAMRecord read, final int offset ) {
byte base;
byte prevBase;
final byte[] bases = read.getReadBases();
// If this is a negative strand read then we need to reverse the direction for our previous base
if( read.getReadNegativeStrandFlag() ) {
// No dinuc at the beginning of the read
if( offset == bases.length-1 ) {
return NO_DINUC;
}
base = (byte)BaseUtils.simpleComplement( (char)(bases[offset]) );
// Note: We are using the previous base in the read, not the previous base in the reference. This is done in part to be consistent with unmapped reads.
prevBase = (byte)BaseUtils.simpleComplement( (char)(bases[offset + 1]) );
} else {
// No dinuc at the beginning of the read
if( offset == 0 ) {
return NO_DINUC;
}
base = bases[offset];
// Note: We are using the previous base in the read, not the previous base in the reference. This is done in part to be consistent with unmapped reads.
prevBase = bases[offset - 1];
}
// Make sure the previous base is good
if( !BaseUtils.isRegularBase( prevBase ) ) {
return NO_DINUC;
}
return dinucHashMap.get( Dinuc.hashBytes( prevBase, base ) );
}
*/
/**
* Takes an array of size (at least) read.getReadLength() and fills it with the covariate values for each position in the read.
*/
public void getValues( SAMRecord read, Comparable[] result ) {
@Override
public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
final HashMap<Integer, Dinuc> dinucHashMapRef = this.dinucHashMap; //optimize access to dinucHashMap
final int readLength = read.getReadLength();
final boolean negativeStrand = read.getReadNegativeStrandFlag();
@ -111,7 +79,7 @@ public class DinucCovariate implements StandardCovariate {
if(negativeStrand) {
bases = BaseUtils.simpleReverseComplement(bases); //this is NOT in-place
}
result[0] = NO_DINUC; // No dinuc at the beginning of the read
comparable[0] = NO_DINUC; // No dinuc at the beginning of the read
prevBase = bases[0];
offset++;
@ -120,20 +88,21 @@ public class DinucCovariate implements StandardCovariate {
// previous base in the reference. This is done in part to be consistent with unmapped reads.
base = bases[offset];
if( BaseUtils.isRegularBase( prevBase ) ) {
result[offset] = dinucHashMapRef.get( Dinuc.hashBytes( prevBase, base ) );
comparable[offset] = dinucHashMapRef.get( Dinuc.hashBytes( prevBase, base ) );
} else {
result[offset] = NO_DINUC;
comparable[offset] = NO_DINUC;
}
offset++;
prevBase = base;
}
if(negativeStrand) {
reverse( result );
reverse( comparable );
}
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
@Override
public final Comparable getValue( final String str ) {
byte[] bytes = str.getBytes();
final Dinuc returnDinuc = dinucHashMap.get( Dinuc.hashBytes( bytes[0], bytes[1] ) );
@ -143,7 +112,6 @@ public class DinucCovariate implements StandardCovariate {
return returnDinuc;
}
/**
* Reverses the given array in place.
*

13
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/GCContentCovariate.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.recalibration;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
/*
* Copyright (c) 2010 The Broad Institute
@ -41,12 +42,13 @@ public class GCContentCovariate implements ExperimentalCovariate {
int numBack = 7;
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize( final RecalibrationArgumentCollection RAC ) {
numBack = RAC.HOMOPOLYMER_NBACK;
}
// Used to pick out the covariate's value from attributes of the read
public final Comparable getValue( final SAMRecord read, final int offset ) {
private final Comparable getValue( final SAMRecord read, final int offset ) {
// ATTGCCCCGTAAAAAAAGAGAA
// 0000123456654321001122
@ -75,18 +77,17 @@ public class GCContentCovariate implements ExperimentalCovariate {
return -1;
}
}
public void getValues(SAMRecord read, Comparable[] comparable) {
@Override
public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
for(int iii = 0; iii < read.getReadLength(); iii++) {
comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
}
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
@Override
public final Comparable getValue( final String str ) {
return Integer.parseInt( str );
}
}

9
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/HomopolymerCovariate.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.recalibration;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
/*
* Copyright (c) 2009 The Broad Institute
@ -43,12 +44,13 @@ public class HomopolymerCovariate implements ExperimentalCovariate {
int numBack = 7;
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize( final RecalibrationArgumentCollection RAC ) {
numBack = RAC.HOMOPOLYMER_NBACK;
}
// Used to pick out the covariate's value from attributes of the read
public final Comparable getValue( final SAMRecord read, final int offset ) {
private final Comparable getValue( final SAMRecord read, final int offset ) {
// This block of code is for if you don't want to only count consecutive bases
// ATTGCCCCGTAAAAAAAAATA
@ -90,15 +92,16 @@ public class HomopolymerCovariate implements ExperimentalCovariate {
return numAgree;
}
public void getValues(SAMRecord read, Comparable[] comparable) {
@Override
public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
for(int iii = 0; iii < read.getReadLength(); iii++) {
comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
}
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
@Override
public final Comparable getValue( final String str ) {
return Integer.parseInt( str );
}
}

9
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.recalibration;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
/*
* Copyright (c) 2009 The Broad Institute
@ -38,23 +39,25 @@ import net.sf.samtools.SAMRecord;
public class MappingQualityCovariate implements ExperimentalCovariate {
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize( final RecalibrationArgumentCollection RAC ) {
}
// Used to pick out the covariate's value from attributes of the read
public final Comparable getValue( final SAMRecord read, final int offset ) {
private final Comparable getValue( final SAMRecord read, final int offset ) {
return read.getMappingQuality();
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
@Override
public final Comparable getValue( final String str ) {
return Integer.parseInt( str );
}
public void getValues(SAMRecord read, Comparable[] comparable) {
@Override
public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
for(int iii = 0; iii < read.getReadLength(); iii++) {
comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
}
}
}

18
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.recalibration;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
/*
* Copyright (c) 2009 The Broad Institute
@ -41,12 +42,13 @@ public class MinimumNQSCovariate implements ExperimentalCovariate {
private int windowReach; // How far in each direction from the current base to look
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize( final RecalibrationArgumentCollection RAC ) {
windowReach = RAC.WINDOW_SIZE / 2; // integer division
}
// Used to pick out the covariate's value from attributes of the read
public final Comparable getValue( final SAMRecord read, final int offset ) {
private final Comparable getValue( final SAMRecord read, final int offset ) {
// Loop over the list of base quality scores in the window and find the minimum
final byte[] quals = read.getBaseQualities();
@ -61,14 +63,16 @@ public class MinimumNQSCovariate implements ExperimentalCovariate {
return minQual;
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
public final Comparable getValue( final String str ) {
return Integer.parseInt( str );
}
public void getValues(SAMRecord read, Comparable[] comparable) {
@Override
public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
for(int iii = 0; iii < read.getReadLength(); iii++) {
comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
}
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
@Override
public final Comparable getValue( final String str ) {
return Integer.parseInt( str );
}
}

17
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.recalibration;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
/*
* Copyright (c) 2009 The Broad Institute
@ -39,11 +40,12 @@ import net.sf.samtools.SAMRecord;
public class PositionCovariate implements ExperimentalCovariate {
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize( final RecalibrationArgumentCollection RAC ) {
}
// Used to pick out the covariate's value from attributes of the read
public final Comparable getValue( final SAMRecord read, final int offset ) {
private final Comparable getValue( final SAMRecord read, final int offset ) {
int cycle = offset;
if( read.getReadNegativeStrandFlag() ) {
cycle = read.getReadLength() - (offset + 1);
@ -51,15 +53,16 @@ public class PositionCovariate implements ExperimentalCovariate {
return cycle;
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
public final Comparable getValue( final String str ) {
return Integer.parseInt( str );
}
public void getValues(SAMRecord read, Comparable[] comparable) {
@Override
public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
for(int iii = 0; iii < read.getReadLength(); iii++) {
comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
}
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
@Override
public final Comparable getValue( final String str ) {
return Integer.parseInt( str );
}
}

18
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java
View File

@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.recalibration;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
/*
* Copyright (c) 2009 The Broad Institute
@ -40,11 +41,12 @@ import net.sf.samtools.SAMRecord;
public class PrimerRoundCovariate implements ExperimentalCovariate {
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize( final RecalibrationArgumentCollection RAC ) {
}
// Used to pick out the covariate's value from attributes of the read
public final Comparable getValue( final SAMRecord read, final int offset ) {
private final Comparable getValue( final SAMRecord read, final int offset ) {
if( read.getReadGroup().getPlatform().equalsIgnoreCase( "SOLID" ) || read.getReadGroup().getPlatform().equalsIgnoreCase( "ABI_SOLID" ) ) {
int pos = offset;
if( read.getReadNegativeStrandFlag() ) {
@ -57,14 +59,16 @@ public class PrimerRoundCovariate implements ExperimentalCovariate {
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
public final Comparable getValue( final String str ) {
return Integer.parseInt( str );
}
public void getValues(SAMRecord read, Comparable[] comparable) {
@Override
public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
for(int iii = 0; iii < read.getReadLength(); iii++) {
comparable[iii] = getValue(read, iii); // BUGBUG: this can be optimized
}
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
@Override
public final Comparable getValue( final String str ) {
return Integer.parseInt( str );
}
}

27
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java
View File

@ -1,6 +1,9 @@
package org.broadinstitute.sting.gatk.walkers.recalibration;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
import java.util.Arrays;
/*
* Copyright (c) 2009 The Broad Institute
@ -38,26 +41,26 @@ import net.sf.samtools.SAMRecord;
public class QualityScoreCovariate implements RequiredCovariate {
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize( final RecalibrationArgumentCollection RAC ) {
}
/*
// Used to pick out the covariate's value from attributes of the read
public final Comparable getValue( final SAMRecord read, final int offset ) {
return (int)(read.getBaseQualities()[offset]);
}
*/
public void getValues(SAMRecord read, Comparable[] comparable) {
byte[] baseQualities = read.getBaseQualities();
for(int i = 0; i < read.getReadLength(); i++) {
comparable[i] = (int) baseQualities[i];
@Override
public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
if( modelType == BaseRecalibration.BaseRecalibrationType.BASE_SUBSTITUTION ) {
byte[] baseQualities = read.getBaseQualities();
for(int i = 0; i < read.getReadLength(); i++) {
comparable[i] = (int) baseQualities[i];
}
} else { // model == BASE_INSERTION || model == BASE_DELETION
Arrays.fill(comparable, 45); // Some day in the future when base insertion and base deletion quals exist the samtools API will
// be updated and the original quals will be pulled here, but for now we assume the original quality is a flat Q45
}
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
@Override
public final Comparable getValue( final String str ) {
return Integer.parseInt( str );
}
}

16
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java
View File

@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.recalibration;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
/*
* Copyright (c) 2009 The Broad Institute
@ -35,22 +36,17 @@ import net.sf.samtools.SAMRecord;
* The Read Group covariate.
*/
public class ReadGroupCovariate implements RequiredCovariate{
public class ReadGroupCovariate implements RequiredCovariate {
public static final String defaultReadGroup = "DefaultReadGroup";
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize( final RecalibrationArgumentCollection RAC ) {
}
/*
// Used to pick out the covariate's value from attributes of the read
public final Comparable getValue( final SAMRecord read, final int offset ) {
return read.getReadGroup().getReadGroupId();
}
*/
public void getValues(SAMRecord read, Comparable[] comparable) {
@Override
public void getValues( final SAMRecord read, final Comparable[] comparable, final BaseRecalibration.BaseRecalibrationType modelType ) {
final String readGroupId = read.getReadGroup().getReadGroupId();
for(int i = 0; i < read.getReadLength(); i++) {
comparable[i] = readGroupId;
@ -58,10 +54,10 @@ public class ReadGroupCovariate implements RequiredCovariate{
}
// Used to get the covariate's value from input csv file in TableRecalibrationWalker
@Override
public final Comparable getValue( final String str ) {
return str;
}
}

5
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
View File

@ -33,6 +33,7 @@ import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.collections.NestedHashMap;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
import org.broadinstitute.sting.utils.sam.AlignmentUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -571,7 +572,7 @@ public class RecalDataManager {
* value for the ith position in the read and the jth covariate in
* reqeustedCovariates list.
*/
public static Comparable[][] computeCovariates(final GATKSAMRecord gatkRead, final List<Covariate> requestedCovariates) {
public static Comparable[][] computeCovariates( final GATKSAMRecord gatkRead, final List<Covariate> requestedCovariates, final BaseRecalibration.BaseRecalibrationType modelType ) {
//compute all covariates for this read
final List<Covariate> requestedCovariatesRef = requestedCovariates;
final int numRequestedCovariates = requestedCovariatesRef.size();
@ -582,7 +583,7 @@ public class RecalDataManager {
// Loop through the list of requested covariates and compute the values of each covariate for all positions in this read
for( int i = 0; i < numRequestedCovariates; i++ ) {
requestedCovariatesRef.get(i).getValues( gatkRead, tempCovariateValuesHolder );
requestedCovariatesRef.get(i).getValues( gatkRead, tempCovariateValuesHolder, modelType );
for(int j = 0; j < readLength; j++) {
//copy values into a 2D array that allows all covar types to be extracted at once for
//an offset j by doing covariateValues_offset_x_covar[j]. This avoids the need to later iterate over covar types.

3
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -39,6 +39,7 @@ import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.collections.NestedHashMap;
import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.text.TextFormattingUtils;
import org.broadinstitute.sting.utils.text.XReadLines;
@ -398,7 +399,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
//compute all covariate values for this read
final Comparable[][] covariateValues_offset_x_covar =
RecalDataManager.computeCovariates(read, requestedCovariates);
RecalDataManager.computeCovariates(read, requestedCovariates, BaseRecalibration.BaseRecalibrationType.BASE_SUBSTITUTION);
// For each base in the read
for( int offset = 0; offset < read.getReadLength(); offset++ ) {

29
public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java
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@ -71,25 +71,24 @@ public class KeepAFSpectrumFrequencySelector extends FrequencyModeSelector {
// recompute AF,AC,AN based on genotypes:
// todo - - maybe too inefficient??
VariantContextUtils.calculateChromosomeCounts(vc, attributes, false);
afArray = new double[] {Double.valueOf((String)attributes.get(VCFConstants.ALLELE_FREQUENCY_KEY))};
} else {
// sites-only vc or we explicitly tell to ignore genotypes; we trust the AF field if present
if ( vc.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) ) {
String afo = vc.getAttributeAsString(VCFConstants.ALLELE_FREQUENCY_KEY, null);
}
if (afo.contains(",")) {
String[] afs = afo.split(",");
afs[0] = afs[0].substring(1,afs[0].length());
afs[afs.length-1] = afs[afs.length-1].substring(0,afs[afs.length-1].length()-1);
// sites-only vc or we explicitly tell to ignore genotypes; we trust the AF field if present
if ( vc.hasAttribute(VCFConstants.ALLELE_FREQUENCY_KEY) ) {
String afo = vc.getAttributeAsString(VCFConstants.ALLELE_FREQUENCY_KEY, null);
afArray = new double[afs.length];
if (afo.contains(",")) {
String[] afs = afo.split(",");
afs[0] = afs[0].substring(1,afs[0].length());
afs[afs.length-1] = afs[afs.length-1].substring(0,afs[afs.length-1].length()-1);
for (int k=0; k < afArray.length; k++)
afArray[k] = Double.valueOf(afs[k]);
}
else
afArray = new double[] {Double.valueOf(afo)};
afArray = new double[afs.length];
for (int k=0; k < afArray.length; k++)
afArray[k] = Double.valueOf(afs[k]);
}
else
afArray = new double[] {Double.valueOf(afo)};
}

4
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
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@ -177,13 +177,13 @@ public class BaseRecalibration {
dataManager.addToAllTables( key, datum, QualityUtils.MIN_USABLE_Q_SCORE ); //BUGBUG: used to be Q5 now is Q6, probably doesn't matter
}
public byte[] recalibrateRead( final GATKSAMRecord read, final byte[] originalQuals ) {
public byte[] recalibrateRead( final GATKSAMRecord read, final byte[] originalQuals, final BaseRecalibrationType modelType ) {
final byte[] recalQuals = originalQuals.clone();
//compute all covariate values for this read
final Comparable[][] covariateValues_offset_x_covar =
RecalDataManager.computeCovariates(read, requestedCovariates);
RecalDataManager.computeCovariates(read, requestedCovariates, modelType);
// For each base in the read
for( int offset = 0; offset < read.getReadLength(); offset++ ) {

11
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.NGSPlatform;
import org.broadinstitute.sting.utils.recalibration.BaseRecalibration;
import java.util.Arrays;
import java.util.HashMap;
@ -162,9 +163,11 @@ public class GATKSAMRecord extends BAMRecord {
return super.equals(o);
}
/*
@Override
public byte[] getBaseQualities() {
return super.getBaseQualities();
/*
if( getAttribute( BQSR_BASES_HAVE_BEEN_RECALIBRATED_TAG ) != null ) {
return super.getBaseQualities();
} else {
@ -178,8 +181,8 @@ public class GATKSAMRecord extends BAMRecord {
return super.getBaseQualities();
}
}
*/
}
*/
/**
* Accessors for base insertion and base deletion quality scores
@ -192,7 +195,7 @@ public class GATKSAMRecord extends BAMRecord {
// if the recal data was populated in the engine then recalibrate the quality scores on the fly
// else give default values which are flat Q45
if( GenomeAnalysisEngine.hasBaseRecalibration() ) {
quals = GenomeAnalysisEngine.getBaseRecalibration().recalibrateRead( this, quals ); // the original quals here are the flat base insertion/deletion quals, NOT the original base qualities
quals = GenomeAnalysisEngine.getBaseRecalibration().recalibrateRead( this, quals, BaseRecalibration.BaseRecalibrationType.BASE_INSERTION ); // the original quals here are the flat base insertion/deletion quals, NOT the original base qualities
}
// add the qual array to the read so that we don't have to do the recalibration work again
setAttribute( BQSR_BASE_INSERTION_QUALITIES, quals );
@ -208,7 +211,7 @@ public class GATKSAMRecord extends BAMRecord {
// if the recal data was populated in the engine then recalibrate the quality scores on the fly
// else give default values which are flat Q45
if( GenomeAnalysisEngine.hasBaseRecalibration() ) {
quals = GenomeAnalysisEngine.getBaseRecalibration().recalibrateRead( this, quals ); // the original quals here are the flat base insertion/deletion quals, NOT the original base qualities
quals = GenomeAnalysisEngine.getBaseRecalibration().recalibrateRead( this, quals, BaseRecalibration.BaseRecalibrationType.BASE_DELETION ); // the original quals here are the flat base insertion/deletion quals, NOT the original base qualities
}
// add the qual array to the read so that we don't have to do the recalibration work again
setAttribute( BQSR_BASE_DELETION_QUALITIES, quals );