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The GenotypingEngine now uses the samples from the mapping of Samples -> PerReadAllele likelihoods instead of passing around a redundant list of samples

This commit is contained in:
Mark DePristo 2013-03-27 09:41:04 -04:00
parent 0310499b65
commit 67cd407854
2 changed files with 11 additions and 18 deletions
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28
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
View File

@ -119,9 +119,10 @@ public class GenotypingEngine {
* Main entry point of class - given a particular set of haplotypes, samples and reference context, compute
* genotype likelihoods and assemble into a list of variant contexts and genomic events ready for calling
*
* The list of samples we're working with is obtained from the haplotypeReadMap
*
* @param UG_engine UG Engine with basic input parameters
* @param haplotypes Haplotypes to assign likelihoods to
* @param samples Samples to genotype
* @param haplotypeReadMap Map from reads->(haplotypes,likelihoods)
* @param perSampleFilteredReadList
* @param ref Reference bytes at active region
@ -136,7 +137,6 @@ public class GenotypingEngine {
// TODO - can this be refactored? this is hard to follow!
public CalledHaplotypes assignGenotypeLikelihoods( final UnifiedGenotyperEngine UG_engine,
final List<Haplotype> haplotypes,
final List<String> samples,
final Map<String, PerReadAlleleLikelihoodMap> haplotypeReadMap,
final Map<String, List<GATKSAMRecord>> perSampleFilteredReadList,
final byte[] ref,
@ -147,7 +147,6 @@ public class GenotypingEngine {
// sanity check input arguments
if (UG_engine == null) throw new IllegalArgumentException("UG_Engine input can't be null, got "+UG_engine);
if (haplotypes == null || haplotypes.isEmpty()) throw new IllegalArgumentException("haplotypes input should be non-empty and non-null, got "+haplotypes);
if (samples == null || samples.isEmpty()) throw new IllegalArgumentException("samples input must be non-empty and non-null, got "+samples);
if (haplotypeReadMap == null || haplotypeReadMap.isEmpty()) throw new IllegalArgumentException("haplotypeReadMap input should be non-empty and non-null, got "+haplotypeReadMap);
if (ref == null || ref.length == 0 ) throw new IllegalArgumentException("ref bytes input should be non-empty and non-null, got "+ref);
if (refLoc == null || refLoc.getStop()-refLoc.getStart()+1 != ref.length) throw new IllegalArgumentException(" refLoc must be non-null and length must match ref bytes, got "+refLoc);
@ -157,7 +156,7 @@ public class GenotypingEngine {
// update the haplotypes so we're ready to call, getting the ordered list of positions on the reference
// that carry events among the haplotypes
final TreeSet<Integer> startPosKeySet = decomposeHaplotypesIntoVariantContexts(haplotypes, samples, haplotypeReadMap, ref, refLoc, activeAllelesToGenotype);
final TreeSet<Integer> startPosKeySet = decomposeHaplotypesIntoVariantContexts(haplotypes, haplotypeReadMap, ref, refLoc, activeAllelesToGenotype);
// Walk along each position in the key set and create each event to be outputted
final Set<Haplotype> calledHaplotypes = new HashSet<Haplotype>();
@ -195,7 +194,7 @@ public class GenotypingEngine {
final Map<String, PerReadAlleleLikelihoodMap> alleleReadMap = convertHaplotypeReadMapToAlleleReadMap( haplotypeReadMap, alleleMapper, UG_engine.getUAC().CONTAMINATION_FRACTION, UG_engine.getUAC().contaminationLog );
final GenotypesContext genotypes = calculateGLsForThisEvent( samples, alleleReadMap, mergedVC );
final GenotypesContext genotypes = calculateGLsForThisEvent( alleleReadMap, mergedVC );
final VariantContext call = UG_engine.calculateGenotypes(new VariantContextBuilder(mergedVC).genotypes(genotypes).make(), mergedVC.isSNP() ? GenotypeLikelihoodsCalculationModel.Model.SNP : GenotypeLikelihoodsCalculationModel.Model.INDEL);
if( call != null ) {
final Map<String, PerReadAlleleLikelihoodMap> alleleReadMap_annotations = ( USE_FILTERED_READ_MAP_FOR_ANNOTATIONS ? alleleReadMap :
@ -224,7 +223,6 @@ public class GenotypingEngine {
* Go through the haplotypes we assembled, and decompose them into their constituent variant contexts
*
* @param haplotypes the list of haplotypes we're working with
* @param samples the samples we're working with
* @param haplotypeReadMap map from samples -> the per read allele likelihoods
* @param ref the reference bases (over the same interval as the haplotypes)
* @param refLoc the span of the reference bases
@ -232,7 +230,6 @@ public class GenotypingEngine {
* @return
*/
private TreeSet<Integer> decomposeHaplotypesIntoVariantContexts(final List<Haplotype> haplotypes,
final List<String> samples,
final Map<String, PerReadAlleleLikelihoodMap> haplotypeReadMap,
final byte[] ref,
final GenomeLoc refLoc,
@ -259,9 +256,9 @@ public class GenotypingEngine {
}
cleanUpSymbolicUnassembledEvents( haplotypes );
if ( !in_GGA_mode && samples.size() >= 10 ) {
if ( !in_GGA_mode && haplotypeReadMap.size() >= 10 ) {
// if not in GGA mode and have at least 10 samples try to create MNP and complex events by looking at LD structure
mergeConsecutiveEventsBasedOnLD( haplotypes, samples, haplotypeReadMap, startPosKeySet, ref, refLoc );
mergeConsecutiveEventsBasedOnLD( haplotypes, haplotypeReadMap, startPosKeySet, ref, refLoc );
cleanUpSymbolicUnassembledEvents( haplotypes ); // the newly created merged events could be overlapping the unassembled events
}
@ -282,7 +279,6 @@ public class GenotypingEngine {
private List<String> makePriorityList(final List<VariantContext> vcs) {
final List<String> priorityList = new LinkedList<String>();
for ( final VariantContext vc : vcs ) priorityList.add(vc.getSource());
return priorityList;
}
@ -333,17 +329,16 @@ public class GenotypingEngine {
/**
* For a particular event described in inputVC, form PL vector for each sample by looking into allele read map and filling likelihood matrix for each allele
* @param samples List of samples to genotype
* @param alleleReadMap Allele map describing mapping from reads to alleles and corresponding likelihoods
* @param mergedVC Input VC with event to genotype
* @return GenotypesContext object wrapping genotype objects with PLs
*/
@Requires({"samples != null","alleleReadMap!= null", "mergedVC != null"})
@Requires({"alleleReadMap!= null", "mergedVC != null"})
@Ensures("result != null")
private GenotypesContext calculateGLsForThisEvent( final List<String> samples, final Map<String, PerReadAlleleLikelihoodMap> alleleReadMap, final VariantContext mergedVC ) {
final GenotypesContext genotypes = GenotypesContext.create(samples.size());
private GenotypesContext calculateGLsForThisEvent( final Map<String, PerReadAlleleLikelihoodMap> alleleReadMap, final VariantContext mergedVC ) {
final GenotypesContext genotypes = GenotypesContext.create(alleleReadMap.size());
// Grab the genotype likelihoods from the appropriate places in the haplotype likelihood matrix -- calculation performed independently per sample
for( final String sample : samples ) {
for( final String sample : alleleReadMap.keySet() ) {
final int numHaplotypes = mergedVC.getAlleles().size();
final double[] genotypeLikelihoods = new double[numHaplotypes * (numHaplotypes+1) / 2];
final double[][] haplotypeLikelihoodMatrix = LikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(sample, alleleReadMap, mergedVC.getAlleles());
@ -448,14 +443,12 @@ public class GenotypingEngine {
/**
* TODO - comment me, clean me, refactor me!
* @param haplotypes
* @param samples
* @param haplotypeReadMap
* @param startPosKeySet
* @param ref
* @param refLoc
*/
protected void mergeConsecutiveEventsBasedOnLD( final List<Haplotype> haplotypes,
final List<String> samples,
final Map<String, PerReadAlleleLikelihoodMap> haplotypeReadMap,
final TreeSet<Integer> startPosKeySet,
final byte[] ref,
@ -465,6 +458,7 @@ public class GenotypingEngine {
final double MERGE_EVENTS_R2_THRESHOLD = 0.95;
if( startPosKeySet.size() <= 1 ) { return; }
final Set<String> samples = haplotypeReadMap.keySet();
boolean mapWasUpdated = true;
while( mapWasUpdated ) {
mapWasUpdated = false;

1
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -559,7 +559,6 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
final GenotypingEngine.CalledHaplotypes calledHaplotypes = genotypingEngine.assignGenotypeLikelihoods( UG_engine,
bestHaplotypes,
samplesList,
stratifiedReadMap,
perSampleFilteredReadList,
fullReferenceWithPadding,