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Now properly extending candidate haplotypes with bases from the reference context instead of filling with padding bases. Functionality in the private Haplotype class is no longer necessary so removing it. No need to have four different Haplotype classes in the GATK.

This commit is contained in:
Ryan Poplin 2011-11-05 12:18:56 -04:00
parent 888d3b4fdc
commit 611a395783
4 changed files with 24 additions and 20 deletions
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10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
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@ -180,12 +180,12 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
final Haplotype haplotype1 = consensusHaplotypeQueue.poll(); final Haplotype haplotype1 = consensusHaplotypeQueue.poll();
List<Haplotype>hlist = new ArrayList<Haplotype>(); List<Haplotype>hlist = new ArrayList<Haplotype>();
hlist.add(new Haplotype(haplotype1.getBasesAsBytes(), 60)); hlist.add(new Haplotype(haplotype1.getBases(), 60));
for (int k=1; k < haplotypesToCompute; k++) { for (int k=1; k < haplotypesToCompute; k++) {
Haplotype haplotype2 = consensusHaplotypeQueue.poll(); Haplotype haplotype2 = consensusHaplotypeQueue.poll();
if(haplotype2 == null ) { haplotype2 = haplotype1; } // Sometimes only the reference haplotype can be found if(haplotype2 == null ) { haplotype2 = haplotype1; } // Sometimes only the reference haplotype can be found
hlist.add(new Haplotype(haplotype2.getBasesAsBytes(), 20)); hlist.add(new Haplotype(haplotype2.getBases(), 20));
} }
return hlist; return hlist;
} else } else
@ -229,8 +229,8 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
} }
private Haplotype getConsensusHaplotype(final Haplotype haplotypeA, final Haplotype haplotypeB) { private Haplotype getConsensusHaplotype(final Haplotype haplotypeA, final Haplotype haplotypeB) {
final byte[] a = haplotypeA.getBasesAsBytes(); final byte[] a = haplotypeA.getBases();
final byte[] b = haplotypeB.getBasesAsBytes(); final byte[] b = haplotypeB.getBases();
if (a.length != b.length) { if (a.length != b.length) {
throw new ReviewedStingException("Haplotypes a and b must be of same length"); throw new ReviewedStingException("Haplotypes a and b must be of same length");
@ -313,7 +313,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
// actually be a miscall in a matching direction, which would happen at a e / 3 rate. If b != c, then // actually be a miscall in a matching direction, which would happen at a e / 3 rate. If b != c, then
// the chance that it is actually a mismatch is 1 - e, since any of the other 3 options would be a mismatch. // the chance that it is actually a mismatch is 1 - e, since any of the other 3 options would be a mismatch.
// so the probability-weighted mismatch rate is sum_i ( matched ? e_i / 3 : 1 - e_i ) for i = 1 ... n // so the probability-weighted mismatch rate is sum_i ( matched ? e_i / 3 : 1 - e_i ) for i = 1 ... n
final byte[] haplotypeBases = haplotype.getBasesAsBytes(); final byte[] haplotypeBases = haplotype.getBases();
final SAMRecord read = p.getRead(); final SAMRecord read = p.getRead();
byte[] readBases = read.getReadBases(); byte[] readBases = read.getReadBases();

18
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
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@ -205,7 +205,7 @@ public class HaplotypeIndelErrorModel {
byte haplotypeBase; byte haplotypeBase;
if (haplotypeIndex < RIGHT_ALIGN_INDEX) if (haplotypeIndex < RIGHT_ALIGN_INDEX)
haplotypeBase = haplotype.getBasesAsBytes()[haplotypeIndex]; haplotypeBase = haplotype.getBases()[haplotypeIndex];
else else
haplotypeBase = (byte)0; // dummy haplotypeBase = (byte)0; // dummy
@ -217,7 +217,7 @@ public class HaplotypeIndelErrorModel {
if (readQual > 3) if (readQual > 3)
pRead += pBaseRead; pRead += pBaseRead;
haplotypeIndex++; haplotypeIndex++;
if (haplotypeIndex >= haplotype.getBasesAsBytes().length) if (haplotypeIndex >= haplotype.getBases().length)
haplotypeIndex = RIGHT_ALIGN_INDEX; haplotypeIndex = RIGHT_ALIGN_INDEX;
//System.out.format("H:%c R:%c RQ:%d HI:%d %4.5f %4.5f\n", haplotypeBase, readBase, (int)readQual, haplotypeIndex, pBaseRead, pRead); //System.out.format("H:%c R:%c RQ:%d HI:%d %4.5f %4.5f\n", haplotypeBase, readBase, (int)readQual, haplotypeIndex, pBaseRead, pRead);
} }
@ -227,8 +227,8 @@ public class HaplotypeIndelErrorModel {
System.out.println(read.getReadName()); System.out.println(read.getReadName());
System.out.print("Haplotype:"); System.out.print("Haplotype:");
for (int k=0; k <haplotype.getBasesAsBytes().length; k++) { for (int k=0; k <haplotype.getBases().length; k++) {
System.out.format("%c ", haplotype.getBasesAsBytes()[k]); System.out.format("%c ", haplotype.getBases()[k]);
} }
System.out.println(); System.out.println();
@ -246,8 +246,8 @@ public class HaplotypeIndelErrorModel {
System.out.println("Haplotype:"); System.out.println("Haplotype:");
for (int k=initialIndexInHaplotype; k <haplotype.getBasesAsBytes().length; k++) { for (int k=initialIndexInHaplotype; k <haplotype.getBases().length; k++) {
System.out.format("%c ", haplotype.getBasesAsBytes()[k]); System.out.format("%c ", haplotype.getBases()[k]);
} }
System.out.println(); System.out.println();
@ -275,7 +275,7 @@ public class HaplotypeIndelErrorModel {
byte haplotypeBase; byte haplotypeBase;
if (indX > LEFT_ALIGN_INDEX && indX < RIGHT_ALIGN_INDEX) if (indX > LEFT_ALIGN_INDEX && indX < RIGHT_ALIGN_INDEX)
haplotypeBase = haplotype.getBasesAsBytes()[indX-1]; haplotypeBase = haplotype.getBases()[indX-1];
else else
haplotypeBase = readBase; haplotypeBase = readBase;
@ -296,8 +296,8 @@ public class HaplotypeIndelErrorModel {
System.out.println(read.getReadName()); System.out.println(read.getReadName());
System.out.print("Haplotype:"); System.out.print("Haplotype:");
for (int k=0; k <haplotype.getBasesAsBytes().length; k++) { for (int k=0; k <haplotype.getBases().length; k++) {
System.out.format("%c ", haplotype.getBasesAsBytes()[k]); System.out.format("%c ", haplotype.getBases()[k]);
} }
System.out.println(); System.out.println();

4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
View File

@ -381,7 +381,7 @@ public class PairHMMIndelErrorModel {
// todo -- refactor into separate function // todo -- refactor into separate function
for (Allele a: haplotypeMap.keySet()) { for (Allele a: haplotypeMap.keySet()) {
Haplotype haplotype = haplotypeMap.get(a); Haplotype haplotype = haplotypeMap.get(a);
byte[] haplotypeBases = haplotype.getBasesAsBytes(); byte[] haplotypeBases = haplotype.getBases();
double[] contextLogGapOpenProbabilities = new double[haplotypeBases.length]; double[] contextLogGapOpenProbabilities = new double[haplotypeBases.length];
double[] contextLogGapContinuationProbabilities = new double[haplotypeBases.length]; double[] contextLogGapContinuationProbabilities = new double[haplotypeBases.length];
@ -555,7 +555,7 @@ public class PairHMMIndelErrorModel {
long indStart = start - haplotype.getStartPosition(); long indStart = start - haplotype.getStartPosition();
long indStop = stop - haplotype.getStartPosition(); long indStop = stop - haplotype.getStartPosition();
byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBasesAsBytes(), byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBases(),
(int)indStart, (int)indStop); (int)indStart, (int)indStop);
double readLikelihood; double readLikelihood;

12
public/java/src/org/broadinstitute/sting/utils/Haplotype.java
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@ -33,8 +33,8 @@ import java.util.LinkedHashMap;
import java.util.List; import java.util.List;
public class Haplotype { public class Haplotype {
protected byte[] bases = null; protected final byte[] bases;
protected double[] quals = null; protected final double[] quals;
private GenomeLoc genomeLocation = null; private GenomeLoc genomeLocation = null;
private boolean isReference = false; private boolean isReference = false;
@ -69,6 +69,11 @@ public class Haplotype {
this.isReference = isRef; this.isReference = isRef;
} }
@Override
public boolean equals( Object h ) {
return h instanceof Haplotype && Arrays.equals(bases, ((Haplotype) h).bases);
}
public double getQualitySum() { public double getQualitySum() {
double s = 0; double s = 0;
for (int k=0; k < bases.length; k++) { for (int k=0; k < bases.length; k++) {
@ -88,7 +93,7 @@ public class Haplotype {
public double[] getQuals() { public double[] getQuals() {
return quals; return quals;
} }
public byte[] getBasesAsBytes() { public byte[] getBases() {
return bases; return bases;
} }
@ -100,7 +105,6 @@ public class Haplotype {
return genomeLocation.getStop(); return genomeLocation.getStop();
} }
public boolean isReference() { public boolean isReference() {
return isReference; return isReference;
} }