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Adding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably.

This commit is contained in:
Ryan Poplin 2012-03-05 08:28:42 -05:00
parent 0ad7d5fbc1
commit d6871967ae
2 changed files with 16 additions and 27 deletions
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36
public/java/src/org/broadinstitute/sting/utils/Haplotype.java
View File

@ -113,24 +113,27 @@ public class Haplotype {
return isReference;
}
public byte[] insertAllele( final Allele refAllele, final Allele altAllele, int refInsertLocation, final byte[] paddedRef, final int refStart,
final Cigar haplotypeCigar, final int numBasesAddedToStartOfHaplotype, final int refHaplotypeLength ) {
public byte[] insertAllele( final Allele refAllele, final Allele altAllele, int refInsertLocation, final int hapStart, final Cigar haplotypeCigar ) {
if( refAllele.length() != altAllele.length() ) { refInsertLocation++; }
int haplotypeInsertLocation = getHaplotypeCoordinateForReferenceCoordinate(refStart + numBasesAddedToStartOfHaplotype, haplotypeCigar, refInsertLocation);
int haplotypeInsertLocation = getHaplotypeCoordinateForReferenceCoordinate(hapStart, haplotypeCigar, refInsertLocation);
if( haplotypeInsertLocation == -1 ) { // desired change falls inside deletion so don't bother creating a new haplotype
return getBases().clone();
return bases.clone();
}
haplotypeInsertLocation += numBasesAddedToStartOfHaplotype;
final byte[] newHaplotype = getBases().clone();
byte[] newHaplotype;
try {
if( refAllele.length() == altAllele.length() ) { // SNP or MNP
newHaplotype = bases.clone();
for( int iii = 0; iii < altAllele.length(); iii++ ) {
newHaplotype[haplotypeInsertLocation+iii] = altAllele.getBases()[iii];
}
} else if( refAllele.length() < altAllele.length() ) { // insertion
} else if( refAllele.length() < altAllele.length() ) { // insertion
final int altAlleleLength = altAllele.length();
newHaplotype = new byte[bases.length + altAlleleLength];
for( int iii = 0; iii < bases.length; iii++ ) {
newHaplotype[iii] = bases[iii];
}
for( int iii = newHaplotype.length - 1; iii > haplotypeInsertLocation + altAlleleLength - 1; iii-- ) {
newHaplotype[iii] = newHaplotype[iii-altAlleleLength];
}
@ -138,24 +141,17 @@ public class Haplotype {
newHaplotype[haplotypeInsertLocation+iii] = altAllele.getBases()[iii];
}
} else { // deletion
int refHaplotypeOffset = 0;
for( final CigarElement ce : haplotypeCigar.getCigarElements()) {
if(ce.getOperator() == CigarOperator.D) { refHaplotypeOffset += ce.getLength(); }
else if(ce.getOperator() == CigarOperator.I) { refHaplotypeOffset -= ce.getLength(); }
}
for( int iii = 0; iii < altAllele.length(); iii++ ) {
newHaplotype[haplotypeInsertLocation+iii] = altAllele.getBases()[iii];
}
final int shift = refAllele.length() - altAllele.length();
for( int iii = haplotypeInsertLocation + altAllele.length(); iii < newHaplotype.length - shift; iii++ ) {
newHaplotype[iii] = newHaplotype[iii+shift];
newHaplotype = new byte[bases.length - shift];
for( int iii = 0; iii < haplotypeInsertLocation + altAllele.length(); iii++ ) {
newHaplotype[iii] = bases[iii];
}
for( int iii = 0; iii < shift; iii++ ) {
newHaplotype[iii+newHaplotype.length-shift] = paddedRef[refStart+refHaplotypeLength+refHaplotypeOffset+iii];
for( int iii = haplotypeInsertLocation + altAllele.length(); iii < newHaplotype.length; iii++ ) {
newHaplotype[iii] = bases[iii+shift];
}
}
} catch (Exception e) { // event already on haplotype is too large/complex to insert another allele, most likely because of not enough reference padding
return getBases().clone();
return bases.clone();
}
return newHaplotype;

7
public/java/test/org/broadinstitute/sting/MedianUnitTest.java
View File

@ -29,7 +29,6 @@ package org.broadinstitute.sting;
// the imports for unit testing.
import org.broadinstitute.sting.gatk.walkers.haplotypecaller.LikelihoodCalculationEngine;
import org.broadinstitute.sting.utils.Median;
import org.testng.Assert;
import org.testng.annotations.BeforeSuite;
@ -42,12 +41,6 @@ import java.util.List;
public class MedianUnitTest extends BaseTest {
LikelihoodCalculationEngine engine;
@BeforeSuite
public void before() {
engine = new LikelihoodCalculationEngine(0, 0, false);
}
// --------------------------------------------------------------------------------
//