From 344083051bcee7cb5481a673fc18d58337711a4a Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Sat, 22 Sep 2012 23:07:28 -0400
Subject: [PATCH] Reverting the fix to the generalized ploidy exact model since
 it cannot handle it computationally.  Will file this in the JIRA.

---
 .../genotyper/GeneralPloidyExactAFCalculationModel.java       | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculationModel.java
index 87572b804..5662d82d6 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculationModel.java
@@ -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;