zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
View File

@ -180,12 +180,12 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
final Haplotype haplotype1 = consensusHaplotypeQueue.poll();
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++) {
Haplotype haplotype2 = consensusHaplotypeQueue.poll();
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;
} else
@ -229,8 +229,8 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
}
private Haplotype getConsensusHaplotype(final Haplotype haplotypeA, final Haplotype haplotypeB) {
final byte[] a = haplotypeA.getBasesAsBytes();
final byte[] b = haplotypeB.getBasesAsBytes();
final byte[] a = haplotypeA.getBases();
final byte[] b = haplotypeB.getBases();
if (a.length != b.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
// 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
final byte[] haplotypeBases = haplotype.getBasesAsBytes();
final byte[] haplotypeBases = haplotype.getBases();
final SAMRecord read = p.getRead();
byte[] readBases = read.getReadBases();

18
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
View File

@ -205,7 +205,7 @@ public class HaplotypeIndelErrorModel {
byte haplotypeBase;
if (haplotypeIndex < RIGHT_ALIGN_INDEX)
haplotypeBase = haplotype.getBasesAsBytes()[haplotypeIndex];
haplotypeBase = haplotype.getBases()[haplotypeIndex];
else
haplotypeBase = (byte)0; // dummy
@ -217,7 +217,7 @@ public class HaplotypeIndelErrorModel {
if (readQual > 3)
pRead += pBaseRead;
haplotypeIndex++;
if (haplotypeIndex >= haplotype.getBasesAsBytes().length)
if (haplotypeIndex >= haplotype.getBases().length)
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);
}
@ -227,8 +227,8 @@ public class HaplotypeIndelErrorModel {
System.out.println(read.getReadName());
System.out.print("Haplotype:");
for (int k=0; k <haplotype.getBasesAsBytes().length; k++) {
System.out.format("%c ", haplotype.getBasesAsBytes()[k]);
for (int k=0; k <haplotype.getBases().length; k++) {
System.out.format("%c ", haplotype.getBases()[k]);
}
System.out.println();
@ -246,8 +246,8 @@ public class HaplotypeIndelErrorModel {
System.out.println("Haplotype:");
for (int k=initialIndexInHaplotype; k <haplotype.getBasesAsBytes().length; k++) {
System.out.format("%c ", haplotype.getBasesAsBytes()[k]);
for (int k=initialIndexInHaplotype; k <haplotype.getBases().length; k++) {
System.out.format("%c ", haplotype.getBases()[k]);
}
System.out.println();
@ -275,7 +275,7 @@ public class HaplotypeIndelErrorModel {
byte haplotypeBase;
if (indX > LEFT_ALIGN_INDEX && indX < RIGHT_ALIGN_INDEX)
haplotypeBase = haplotype.getBasesAsBytes()[indX-1];
haplotypeBase = haplotype.getBases()[indX-1];
else
haplotypeBase = readBase;
@ -296,8 +296,8 @@ public class HaplotypeIndelErrorModel {
System.out.println(read.getReadName());
System.out.print("Haplotype:");
for (int k=0; k <haplotype.getBasesAsBytes().length; k++) {
System.out.format("%c ", haplotype.getBasesAsBytes()[k]);
for (int k=0; k <haplotype.getBases().length; k++) {
System.out.format("%c ", haplotype.getBases()[k]);
}
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
for (Allele a: haplotypeMap.keySet()) {
Haplotype haplotype = haplotypeMap.get(a);
byte[] haplotypeBases = haplotype.getBasesAsBytes();
byte[] haplotypeBases = haplotype.getBases();
double[] contextLogGapOpenProbabilities = new double[haplotypeBases.length];
double[] contextLogGapContinuationProbabilities = new double[haplotypeBases.length];
@ -555,7 +555,7 @@ public class PairHMMIndelErrorModel {
long indStart = start - haplotype.getStartPosition();
long indStop = stop - haplotype.getStartPosition();
byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBasesAsBytes(),
byte[] haplotypeBases = Arrays.copyOfRange(haplotype.getBases(),
(int)indStart, (int)indStop);
double readLikelihood;

12
public/java/src/org/broadinstitute/sting/utils/Haplotype.java
View File

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