From 0fbd40aecc76985cb71a80676a348da512dbf372 Mon Sep 17 00:00:00 2001
From: Paul Wolfe <P.Wolfe@hartwigmedicalfoundation.nl>
Date: Thu, 7 Feb 2019 10:57:32 +0100
Subject: [PATCH] Dump heap on memory error in realignment

Adding these options to help us get to the bottom of memory issues in
P5. They should not have any impact if there is no OOM error.
---
 templates/Realignment.sh.tt | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/templates/Realignment.sh.tt b/templates/Realignment.sh.tt
index 468c46f..0de130b 100644
--- a/templates/Realignment.sh.tt
+++ b/templates/Realignment.sh.tt
@@ -9,6 +9,8 @@ cd "[% dirs.tmp %]"
 assert_not_empty "[% sample_bam_path %]"
 
 java -Xmx[% opt.REALIGNMENT_MASTER_MEM %]G \
+    -XX:+HeapDumpOnOutOfMemoryError \
+    -XX:HeapDumpPath="[% opt.OUTPUT_DIR %]" \
     -Djava.io.tmpdir="[% dirs.tmp %]" \
     -jar "[% opt.GATK_QUEUE_PATH %]/Queue.jar" \
     -jobQueue [% opt.REALIGNMENT_QUEUE %] \