From d9f5a314ac3f49c1caa30601ba9125770b5a48ba Mon Sep 17 00:00:00 2001
From: jmaguire <jmaguire@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 9 Oct 2009 14:56:55 +0000
Subject: [PATCH] avoid an out of memory error by no putting more than 5000
 reads in the cache. on pilot1 at least those are crazy loci anyway.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1802 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/MultiSampleCaller2.java        | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller2.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller2.java
index d44aef7ea..2785a3477 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller2.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller2.java
@@ -242,7 +242,7 @@ public class MultiSampleCaller2 extends LocusWalker<MultiSampleCaller2.MultiSamp
 
 			if (SAMPLE_NAME_REGEX != null) { sample_name = sample_name.replaceAll(SAMPLE_NAME_REGEX, "$1"); }
 
-            System.out.printf("SAMPLE: %s %s\n", sample_name, platform);
+            //System.out.printf("SAMPLE: %s %s\n", sample_name, platform);
 
 			if (unique_sample_names.contains(sample_name)) { continue; }
 			unique_sample_names.add(sample_name);
@@ -362,6 +362,7 @@ public class MultiSampleCaller2 extends LocusWalker<MultiSampleCaller2.MultiSamp
 	}
 	
 	HashMap<AlignmentContext, ClassicGenotypeLikelihoods> glCache = new HashMap<AlignmentContext, ClassicGenotypeLikelihoods>();
+	int cache_size = 0;
 
     ClassicGenotypeLikelihoods GenotypeOld(AlignmentContext context, double[] allele_likelihoods, double indel_alt_freq) {
         //ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
@@ -441,7 +442,16 @@ public class MultiSampleCaller2 extends LocusWalker<MultiSampleCaller2.MultiSamp
                 G = (ClassicGenotypeLikelihoods)cached.clone();
             } else {
                 G = reallyMakeGenotypeLikelihood(context);
-                glCache.put(context, G.clone());
+				if (cache_size < 5000)
+				{
+					//System.out.printf("cache add (%d)\n", cache_size);
+                	glCache.put(context, G.clone());
+					cache_size += context.getReads().size();
+				}
+				else
+				{
+					//System.out.printf("cache skip (%d)\n", cache_size);
+				}
             }
             G.ApplyPrior(ref, allele_likelihoods);
         }
@@ -827,7 +837,8 @@ public class MultiSampleCaller2 extends LocusWalker<MultiSampleCaller2.MultiSamp
 		if (tracker.lookup("DBSNP", null) != null) { in_dbsnp = "known"; } else { in_dbsnp = "novel"; }
 
 		AlignmentContext[] contexts = filterAlignmentContext(context, sample_names, 0);
-		glCache.clear(); // reset the contexts
+		glCache.clear(); // reset the cache
+		cache_size = 0;
 		
 		double lod = LOD(contexts);