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Reverting the fix to the generalized ploidy exact model since it cannot handle it computationally. Will file this in the JIRA.

This commit is contained in:
Eric Banks 2012-09-22 23:07:28 -04:00
parent 25e3ea879a
commit 344083051b
1 changed files with 3 additions and 1 deletions
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4
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculationModel.java
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@ -281,7 +281,9 @@ public class GeneralPloidyExactAFCalculationModel extends AlleleFrequencyCalcula
if (!Double.isInfinite(log10LofK))
newPool.add(set);
if ( log10LofK < maxLikelihoodSeen.maxLog10L - MAX_LOG10_ERROR_TO_STOP_EARLY && maxLikelihoodSeen.isLowerAC(set.ACcounts) ) {
// TODO -- uncomment this correct line when the implementation of this model is optimized (it's too slow now to handle this fix)
//if ( log10LofK < maxLikelihoodSeen.maxLog10L - MAX_LOG10_ERROR_TO_STOP_EARLY && maxLikelihoodSeen.isLowerAC(set.ACcounts) ) {
if ( log10LofK < maxLikelihoodSeen.maxLog10L - MAX_LOG10_ERROR_TO_STOP_EARLY ) {
if ( VERBOSE )
System.out.printf(" *** breaking early set=%s log10L=%.2f maxLog10L=%.2f%n", set.ACcounts, log10LofK, maxLikelihoodSeen.maxLog10L);
return log10LofK;