From 6cb10cef9638fe4d57cfe6168cb11fa3be8c2230 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 31 Jul 2012 16:00:36 -0400
Subject: [PATCH] Fixed older GS reported bug.  Actually, the problem really
 lies in Picard (can't set max records in RAM without it throwing an
 exception, reported on their JIRA) so I just masked out the problem by
 removing this never-used argument from this rarely-used tool.

---
 .../gatk/io/storage/SAMFileWriterStorage.java      |  1 +
 .../sting/gatk/walkers/indels/LeftAlignIndels.java | 14 +-------------
 2 files changed, 2 insertions(+), 13 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
index cb8786be1..300e801e6 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
@@ -62,6 +62,7 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
         if (stub.getGenerateMD5())
             factory.setCreateMd5File(true);
         // Adjust max records in RAM.
+        // TODO -- this doesn't actually work because of a bug in Picard; do not use until fixed
         if(stub.getMaxRecordsInRam() != null)
             factory.setMaxRecordsInRam(stub.getMaxRecordsInRam());
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
index 6047a15b4..b08def44f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
@@ -73,19 +73,7 @@ public class LeftAlignIndels extends ReadWalker<Integer, Integer> {
     @Output(required=false, doc="Output bam")
     protected StingSAMFileWriter writer = null;
 
-    /**
-     * If set too low, the tool may run out of system file descriptors needed to perform sorting; if too high, the tool
-     * may run out of memory.  We recommend that you additionally tell Java to use a temp directory with plenty of available
-     * space (by setting java.io.tempdir on the command-line).
-     */
-    @Argument(fullName="maxReadsInRam", shortName="maxInRam", doc="max reads allowed to be kept in memory at a time by the output writer", required=false)
-    protected int MAX_RECORDS_IN_RAM = 500000;
-
-    public void initialize() {
-        // set up the output writer
-        if ( writer != null )
-            writer.setMaxRecordsInRam(MAX_RECORDS_IN_RAM);
-    }
+    public void initialize() {}
 
     private void emit(final SAMRecord read) {
         if ( writer != null )