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ReducedRead optimization: single pass likelihood calculation 

-- Low level add() now takes a nObs argument and rather than += likelihood now does += nObs * likelihood
This commit is contained in:
Mark DePristo 2011-08-09 20:55:15 -04:00
parent afd0b5b383
commit 86afe878a7
1 changed files with 12 additions and 14 deletions
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26
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
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@ -276,13 +276,11 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
if ( elt.isReducedRead() ) { if ( elt.isReducedRead() ) {
// reduced read representation // reduced read representation
byte qual = elt.getReducedQual(); byte qual = elt.getReducedQual();
for ( int i = 0; i < elt.getReducedCount(); i++ ) { add(obsBase, qual, (byte)0, (byte)0, elt.getReducedCount()); // fast calculation of n identical likelihoods
add(obsBase, qual, (byte)0, (byte)0); return elt.getReducedCount(); // we added nObs bases here
}
return elt.getQual();
} else { } else {
byte qual = qualToUse(elt, ignoreBadBases, capBaseQualsAtMappingQual, minBaseQual); byte qual = qualToUse(elt, ignoreBadBases, capBaseQualsAtMappingQual, minBaseQual);
return qual > 0 ? add(obsBase, qual, (byte)0, (byte)0) : 0; return qual > 0 ? add(obsBase, qual, (byte)0, (byte)0, 1) : 0;
} }
} }
@ -309,9 +307,11 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
* @param qual1 * @param qual1
* @param obsBase2 * @param obsBase2
* @param qual2 can be 0, indicating no second base was observed for this fragment * @param qual2 can be 0, indicating no second base was observed for this fragment
* @param nObs The number of times this quad of values was seen. Generally 1, but reduced reads
* can have nObs > 1 for synthetic reads
* @return * @return
*/ */
private int add(byte obsBase1, byte qual1, byte obsBase2, byte qual2) { private int add(byte obsBase1, byte qual1, byte obsBase2, byte qual2, int nObs) {
// TODO-- Right now we assume that there are at most 2 reads per fragment. This assumption is fine // TODO-- Right now we assume that there are at most 2 reads per fragment. This assumption is fine
// TODO-- given the current state of next-gen sequencing, but may need to be fixed in the future. // TODO-- given the current state of next-gen sequencing, but may need to be fixed in the future.
// TODO-- However, when that happens, we'll need to be a lot smarter about the caching we do here. // TODO-- However, when that happens, we'll need to be a lot smarter about the caching we do here.
@ -332,19 +332,17 @@ public class DiploidSNPGenotypeLikelihoods implements Cloneable {
for ( DiploidGenotype g : DiploidGenotype.values() ) { for ( DiploidGenotype g : DiploidGenotype.values() ) {
double likelihood = likelihoods[g.ordinal()]; double likelihood = likelihoods[g.ordinal()];
log10Likelihoods[g.ordinal()] += likelihood * nObs;
//if ( VERBOSE ) { log10Posteriors[g.ordinal()] += likelihood * nObs;
// System.out.printf(" L(%c | G=%s, Q=%d, S=%s) = %f / %f%n",
// observedBase, g, qualityScore, pow(10,likelihood) * 100, likelihood);
//}
log10Likelihoods[g.ordinal()] += likelihood;
log10Posteriors[g.ordinal()] += likelihood;
} }
return 1; return 1;
} }
private int add(byte obsBase1, byte qual1, byte obsBase2, byte qual2) {
return add(obsBase1, qual1, obsBase2, qual2, 1);
}
// ------------------------------------------------------------------------------------- // -------------------------------------------------------------------------------------
// //
// Dealing with the cache routines // Dealing with the cache routines