From 52a36f282ca3896ae9523217581bd11ede0b305a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 14 Feb 2015 16:28:52 +0100
Subject: [PATCH] Fix threads / memlimit
---
.../nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
index 18b4f0641..9521e9ea0 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
@@ -41,7 +41,7 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
threads = 1
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
}
- nct = Some(threads)
+ nct = Some(getThreads(1))
memoryLimit = Option(memoryLimit.getOrElse(2.0) * nct.getOrElse(1))
}
diff --git a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
index 684c2123a..599ffa170 100644
--- a/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
+++ b/protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
@@ -15,7 +15,7 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
if (config.contains("scattercount")) scatterCount = config("scattercount")
if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
this.sample_ploidy = config("ploidy")
- nct = config("threads", default = 1)
+ nct = Some(getThreads(1))
memoryLimit = Option(nct.getOrElse(1) * 2)
if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
if (config.contains("output_mode")) {
--
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