From 25e1302fb76bd2200122b62ba07a4512e24bf486 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 7 Aug 2014 16:27:16 +0200
Subject: [PATCH] Added config option targetBed
---
.../lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index d0ec70ad7..e2b0452a3 100644
--- a/bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/bam-metrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -29,6 +29,11 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
for (file <- configfiles) globalConfig.loadConfigFile(file)
if (outputDir == null) throw new IllegalStateException("Missing Output directory on BamMetrics module")
else if (!outputDir.endsWith("/")) outputDir += "/"
+ if (configContains("targetBed")) {
+ for (file <- config("targetBed").getList) {
+ bedFiles +:= new File(file.toString)
+ }
+ }
}
def biopetScript() {
--
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