From 6585ec2e123f76384a35feb332b6dcf0d600118a Mon Sep 17 00:00:00 2001
From: Daniel Cameron <daniel.l.cameron@gmail.com>
Date: Thu, 11 Oct 2018 22:55:12 +1100
Subject: [PATCH] Bug fix: CollectGridssMetricsAndExtractSVReads was not
 passing INCLUDE_DUPLICATES command line parameter to ExtractSVReads

---
 src/main/java/gridss/CollectGridssMetricsAndExtractSVReads.java | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/main/java/gridss/CollectGridssMetricsAndExtractSVReads.java b/src/main/java/gridss/CollectGridssMetricsAndExtractSVReads.java
index 619a5b3d4..cca6a434f 100644
--- a/src/main/java/gridss/CollectGridssMetricsAndExtractSVReads.java
+++ b/src/main/java/gridss/CollectGridssMetricsAndExtractSVReads.java
@@ -81,6 +81,7 @@ protected ExtractSVReads getExtractSVReads() {
     	extract.READ_PAIR_CONCORDANT_PERCENT = READ_PAIR_CONCORDANT_PERCENT;
     	extract.INSERT_SIZE_METRICS = INSERT_SIZE_METRICS;
     	extract.UNMAPPED_READS = UNMAPPED_READS;
+        extract.INCLUDE_DUPLICATES = INCLUDE_DUPLICATES;
     	extract.METRICS_OUTPUT = METRICS_OUTPUT;
     	extract.OUTPUT = SV_OUTPUT;
     	extract.INPUT = this.INPUT;