From b9f88a3950677a21a315a1a4afa513e5e70bbac0 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 5 Feb 2015 16:28:27 +0100
Subject: [PATCH] Minor code refactor
---
.../sasc/biopet/extensions/gatk/HaplotypeCaller.scala | 10 +++++-----
1 file changed, 5 insertions(+), 5 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 953bf02b5..b8f4ea4ef 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
@@ -10,13 +10,11 @@ import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral {
min_mapping_quality_score = config("minMappingQualityScore", default = 20)
- if (config.contains("scattercount")) scatterCount = config("scattercount")
+ scatterCount = config("scattercount", default = 1)
if (config.contains("dbsnp")) this.dbsnp = config("dbsnp")
this.sample_ploidy = config("ploidy")
- nct = config("threads", default = 1)
if (config.contains("bamOutput")) bamOutput = config("bamOutput")
- memoryLimit = Option(nct.getOrElse(1) * 2)
- if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
+ if (config.contains("allSitePLs")) allSitePLs = config("allSitePLs")
if (config.contains("output_mode")) {
import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
config("output_mode").asString match {
@@ -40,9 +38,11 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
override def afterGraph {
super.afterGraph
if (bamOutput != null && nct.getOrElse(1) > 1) {
- nct = Option(1)
+ threads = 1
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
}
+ nct = Some(threads)
+ memoryLimit = Option(memoryLimit.getOrElse(2.0) * nct.getOrElse(1))
}
def useGvcf() {
--
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