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Context covariate now operates as a highly compressed bitset 

* All contexts with 'N' bases are now collapsed as uninformative
   * Context size is now represented internally as a BitSet but output as a dna string
   * Temporarily disabled sorted outputs because of null objects
This commit is contained in:
Mauricio Carneiro 2012-02-29 18:56:11 -05:00
parent d379c3763a
commit 9e95b10789
6 changed files with 35 additions and 43 deletions
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54
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ContextCovariate.java
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@ -26,10 +26,12 @@
package org.broadinstitute.sting.gatk.walkers.bqsr;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.Arrays;
import java.util.BitSet;
/**
* Created by IntelliJ IDEA.
@ -43,10 +45,6 @@ public class ContextCovariate implements StandardCovariate {
private int insertionsContextSize;
private int deletionsContextSize;
private String mismatchesNoContext = "";
private String insertionsNoContext = "";
private String deletionsNoContext = "";
// Initialize any member variables using the command-line arguments passed to the walkers
@Override
public void initialize(final RecalibrationArgumentCollection RAC) {
@ -57,29 +55,26 @@ public class ContextCovariate implements StandardCovariate {
if (mismatchesContextSize <= 0 || insertionsContextSize <= 0 || deletionsContextSize <= 0)
throw new UserException(String.format("Context Size must be positive, if you don't want to use the context covariate, just turn it off instead. Mismatches: %d Insertions: %d Deletions:%d", mismatchesContextSize, insertionsContextSize, deletionsContextSize));
// initialize no context strings given the size of the context for each covariate type
mismatchesNoContext = makeAllNStringWithLength(mismatchesContextSize);
insertionsNoContext = makeAllNStringWithLength(insertionsContextSize);
deletionsNoContext = makeAllNStringWithLength( deletionsContextSize);
}
@Override
public CovariateValues getValues(final GATKSAMRecord read) {
int l = read.getReadLength();
String[] mismatches = new String [l];
String[] insertions = new String [l];
String[] deletions = new String [l];
BitSet[] mismatches = new BitSet[l];
BitSet[] insertions = new BitSet[l];
BitSet[] deletions = new BitSet[l];
final boolean negativeStrand = read.getReadNegativeStrandFlag();
byte[] bases = read.getReadBases();
if (negativeStrand) {
bases = BaseUtils.simpleReverseComplement(bases); //this is NOT in-place
}
if (negativeStrand)
bases = BaseUtils.simpleReverseComplement(bases);
for (int i = 0; i < read.getReadLength(); i++) {
mismatches[i] = contextWith(bases, i, mismatchesContextSize, mismatchesNoContext);
insertions[i] = contextWith(bases, i, insertionsContextSize, insertionsNoContext);
deletions[i] = contextWith(bases, i, deletionsContextSize, deletionsNoContext);
mismatches[i] = contextWith(bases, i, mismatchesContextSize);
insertions[i] = contextWith(bases, i, insertionsContextSize);
deletions[i] = contextWith(bases, i, deletionsContextSize);
}
if (negativeStrand) {
reverse(mismatches);
reverse(insertions);
@ -90,7 +85,7 @@ public class ContextCovariate implements StandardCovariate {
// Used to get the covariate's value from input csv file during on-the-fly recalibration
@Override
public final Comparable getValue(final String str) {
public final Object getValue(final String str) {
return str;
}
@ -100,29 +95,28 @@ public class ContextCovariate implements StandardCovariate {
* @param bases the bases in the read to build the context from
* @param offset the position in the read to calculate the context for
* @param contextSize context size to use building the context
* @param noContextString string to return if the position is not far enough in the read to have a full context before.
* @return
*/
private String contextWith(byte [] bases, int offset, int contextSize, String noContextString) {
return (offset < contextSize) ? noContextString : new String(Arrays.copyOfRange(bases, offset - contextSize, offset));
private BitSet contextWith(byte [] bases, int offset, int contextSize) {
if (offset < contextSize)
return null;
String context = new String(Arrays.copyOfRange(bases, offset - contextSize, offset));
if (context.contains("N"))
return null;
return MathUtils.bitSetFrom(context);
}
private String makeAllNStringWithLength(int length) {
String s = "";
for (int i=0; i<length; i++)
s += "N";
return s;
}
/**
* Reverses the given array in place.
*
* @param array any array
*/
private static void reverse(final Comparable[] array) {
private static void reverse(final Object[] array) {
final int arrayLength = array.length;
for (int l = 0, r = arrayLength - 1; l < r; l++, r--) {
final Comparable temp = array[l];
final Object temp = array[l];
array[l] = array[r];
array[r] = temp;
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/Covariate.java
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@ -53,7 +53,7 @@ public interface Covariate {
*/
public CovariateValues getValues(GATKSAMRecord read);
public Comparable getValue(String str); // Used to get the covariate's value from input csv file during on-the-fly recalibration
public Object getValue(String str); // Used to get the covariate's value from input csv file during on-the-fly recalibration
}
interface RequiredCovariate extends Covariate {}

14
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CovariateValues.java
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@ -12,25 +12,25 @@ package org.broadinstitute.sting.gatk.walkers.bqsr;
* @since 2/8/12
*/
public class CovariateValues {
private Comparable[] mismatches;
private Comparable[] insertions;
private Comparable[] deletions;
private Object[] mismatches;
private Object[] insertions;
private Object[] deletions;
public CovariateValues(Comparable[] mismatch, Comparable[] insertion, Comparable[] deletion) {
public CovariateValues(Object[] mismatch, Object[] insertion, Object[] deletion) {
this.mismatches = mismatch;
this.insertions = insertion;
this.deletions = deletion;
}
public Comparable[] getMismatches() {
public Object[] getMismatches() {
return mismatches;
}
public Comparable[] getInsertions() {
public Object[] getInsertions() {
return insertions;
}
public Comparable[] getDeletions() {
public Object[] getDeletions() {
return deletions;
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/CycleCovariate.java
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@ -198,7 +198,7 @@ public class CycleCovariate implements StandardCovariate {
// Used to get the covariate's value from input csv file during on-the-fly recalibration
@Override
public final Comparable getValue(final String str) {
public final Object getValue(final String str) {
return Integer.parseInt(str);
}
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/QualityScoreCovariate.java
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@ -2,8 +2,6 @@ package org.broadinstitute.sting.gatk.walkers.bqsr;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.Arrays;
/*
* Copyright (c) 2009 The Broad Institute
*
@ -67,7 +65,7 @@ public class QualityScoreCovariate implements RequiredCovariate {
// Used to get the covariate's value from input csv file during on-the-fly recalibration
@Override
public final Comparable getValue(final String str) {
public final Object getValue(final String str) {
return Integer.parseInt(str);
}
}

2
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/ReadGroupCovariate.java
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@ -55,7 +55,7 @@ public class ReadGroupCovariate implements RequiredCovariate {
// Used to get the covariate's value from input csv file during on-the-fly recalibration
@Override
public final Comparable getValue(final String str) {
public final Object getValue(final String str) {
return str;
}
}