From 99ad7b2d7136080fd12ce4c4f303e44e058b4160 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 5 Oct 2012 11:49:27 -0700
Subject: [PATCH] GeneralPloidyExact should use indel max alt alleles

---
 .../gatk/walkers/genotyper/GeneralPloidyExactAFCalculation.java | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculation.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculation.java
index f1e38720c..1a51598e2 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculation.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculation.java
@@ -53,6 +53,8 @@ public class GeneralPloidyExactAFCalculation extends ExactAFCalculation {
 
     @Override
     protected VariantContext reduceScope(VariantContext vc) {
+        final int maxAltAlleles = vc.getType().equals(VariantContext.Type.INDEL) ? MAX_ALTERNATE_ALLELES_FOR_INDELS : MAX_ALTERNATE_ALLELES_TO_GENOTYPE;
+
         // don't try to genotype too many alternate alleles
         if ( vc.getAlternateAlleles().size() > maxAltAlleles) {
             logger.warn("this tool is currently set to genotype at most " + maxAltAlleles + " alternate alleles in a given context, but the context at " + vc.getChr() + ":" + vc.getStart() + " has " + (vc.getAlternateAlleles().size()) + " alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument");