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Adding Genotype Given Alleles mode to the HaplotypeCaller. It constructs the possible haplotypes via assembly and then injects the desired allele to be genotyped.

This commit is contained in:
Ryan Poplin 2012-02-18 10:31:26 -05:00
parent 30085781cf
commit 78718b8d6a
2 changed files with 133 additions and 4 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
View File

@ -69,8 +69,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
for(int iii = prevLoc.getStart() + 1; iii < location.getStart(); iii++ ) {
final GenomeLoc fakeLoc = engine.getGenomeLocParser().createGenomeLoc(prevLoc.getContig(), iii, iii);
if( initialIntervals == null || initialIntervals.overlaps( fakeLoc ) ) {
final double isActiveProb = ( walker.presetActiveRegions == null ? walker.isActive( null, null, null )
: ( walker.presetActiveRegions.overlaps(fakeLoc) ? 1.0 : 0.0 ) );
final double isActiveProb = ( walker.presetActiveRegions == null ? 0.0 : ( walker.presetActiveRegions.overlaps(fakeLoc) ? 1.0 : 0.0 ) );
isActiveList.add( isActiveProb );
if( firstIsActiveStart == null ) {
firstIsActiveStart = fakeLoc;

134
public/java/src/org/broadinstitute/sting/utils/Haplotype.java
View File

@ -24,11 +24,17 @@
package org.broadinstitute.sting.utils;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import java.util.Arrays;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
@ -109,8 +115,52 @@ public class Haplotype {
return isReference;
}
public byte[] insertAllele( final Allele a ) {
return getBases();
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 ) {
if( refAllele.length() != altAllele.length() ) { refInsertLocation++; }
int haplotypeInsertLocation = getHaplotypeCoordinateForReferenceCoordinate(refStart + numBasesAddedToStartOfHaplotype, haplotypeCigar, refInsertLocation);
if( haplotypeInsertLocation == -1 ) { // desired change falls inside deletion so don't bother creating a new haplotype
return getBases().clone();
}
haplotypeInsertLocation += numBasesAddedToStartOfHaplotype;
final byte[] newHaplotype = getBases().clone();
try {
if( refAllele.length() == altAllele.length() ) { // SNP or MNP
for( int iii = 0; iii < altAllele.length(); iii++ ) {
newHaplotype[haplotypeInsertLocation+iii] = altAllele.getBases()[iii];
}
} else if( refAllele.length() < altAllele.length() ) { // insertion
final int altAlleleLength = altAllele.length();
for( int iii = newHaplotype.length -1; iii > haplotypeInsertLocation + altAlleleLength; iii-- ) {
newHaplotype[iii] = newHaplotype[iii-altAlleleLength];
}
for( int iii = 0; iii < altAlleleLength; iii++ ) {
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];
}
for( int iii = 0; iii < shift; iii++ ) {
newHaplotype[iii+newHaplotype.length-shift] = paddedRef[refStart+refHaplotypeLength+refHaplotypeOffset+iii];
}
}
} 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 newHaplotype;
}
public static LinkedHashMap<Allele,Haplotype> makeHaplotypeListFromAlleles(List<Allele> alleleList, int startPos, ReferenceContext ref,
@ -169,4 +219,84 @@ public class Haplotype {
return haplotypeMap;
}
private static Integer getHaplotypeCoordinateForReferenceCoordinate( final int haplotypeStart, final Cigar haplotypeCigar, final int refCoord ) {
int readBases = 0;
int refBases = 0;
boolean fallsInsideDeletion = false;
int goal = refCoord - haplotypeStart; // The goal is to move this many reference bases
boolean goalReached = refBases == goal;
Iterator<CigarElement> cigarElementIterator = haplotypeCigar.getCigarElements().iterator();
while (!goalReached && cigarElementIterator.hasNext()) {
CigarElement cigarElement = cigarElementIterator.next();
int shift = 0;
if (cigarElement.getOperator().consumesReferenceBases() || cigarElement.getOperator() == CigarOperator.SOFT_CLIP) {
if (refBases + cigarElement.getLength() < goal)
shift = cigarElement.getLength();
else
shift = goal - refBases;
refBases += shift;
}
goalReached = refBases == goal;
if (!goalReached && cigarElement.getOperator().consumesReadBases())
readBases += cigarElement.getLength();
if (goalReached) {
// Is this base's reference position within this cigar element? Or did we use it all?
boolean endsWithinCigar = shift < cigarElement.getLength();
// If it isn't, we need to check the next one. There should *ALWAYS* be a next one
// since we checked if the goal coordinate is within the read length, so this is just a sanity check.
if (!endsWithinCigar && !cigarElementIterator.hasNext())
return -1;
CigarElement nextCigarElement;
// if we end inside the current cigar element, we just have to check if it is a deletion
if (endsWithinCigar)
fallsInsideDeletion = cigarElement.getOperator() == CigarOperator.DELETION;
// if we end outside the current cigar element, we need to check if the next element is an insertion or deletion.
else {
nextCigarElement = cigarElementIterator.next();
// if it's an insertion, we need to clip the whole insertion before looking at the next element
if (nextCigarElement.getOperator() == CigarOperator.INSERTION) {
readBases += nextCigarElement.getLength();
if (!cigarElementIterator.hasNext())
return -1;
nextCigarElement = cigarElementIterator.next();
}
// if it's a deletion, we will pass the information on to be handled downstream.
fallsInsideDeletion = nextCigarElement.getOperator() == CigarOperator.DELETION;
}
// If we reached our goal outside a deletion, add the shift
if (!fallsInsideDeletion && cigarElement.getOperator().consumesReadBases())
readBases += shift;
// If we reached our goal inside a deletion, but the deletion is the next cigar element then we need
// to add the shift of the current cigar element but go back to it's last element to return the last
// base before the deletion (see warning in function contracts)
else if (fallsInsideDeletion && !endsWithinCigar)
readBases += shift - 1;
// If we reached our goal inside a deletion then we must backtrack to the last base before the deletion
else if (fallsInsideDeletion && endsWithinCigar)
readBases--;
}
}
if (!goalReached)
return -1;
return (fallsInsideDeletion ? -1 : readBases);
}
}