From c008141f2d2b3211cd3d00084dae95433b924bd3 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 5 Feb 2015 15:13:47 +0100
Subject: [PATCH] Fix some options
---
.../extensions/gatk/HaplotypeCaller.scala | 56 +++++++++----------
1 file changed, 28 insertions(+), 28 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 001fb9d17..953bf02b5 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
@@ -9,36 +9,36 @@ import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.HaplotypeCaller with GatkGeneral {
- override def afterGraph {
- super.afterGraph
-
- min_mapping_quality_score = config("minMappingQualityScore", default = 20)
- 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)
- bamOutput = config("bamOutput")
- memoryLimit = Option(nct.getOrElse(1) * 2)
- if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
- if (config.contains("output_mode")) {
- import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
- config("output_mode").asString match {
- case "EMIT_ALL_CONFIDENT_SITES" => output_mode = EMIT_ALL_CONFIDENT_SITES
- case "EMIT_ALL_SITES" => output_mode = EMIT_ALL_SITES
- case "EMIT_VARIANTS_ONLY" => output_mode = EMIT_VARIANTS_ONLY
- case e => logger.warn("output mode '" + e + "' does not exist")
- }
+ min_mapping_quality_score = config("minMappingQualityScore", default = 20)
+ 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)
+ if (config.contains("bamOutput")) bamOutput = config("bamOutput")
+ memoryLimit = Option(nct.getOrElse(1) * 2)
+ if (config.contains("allSitePLs")) this.allSitePLs = config("allSitePLs")
+ if (config.contains("output_mode")) {
+ import org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
+ config("output_mode").asString match {
+ case "EMIT_ALL_CONFIDENT_SITES" => output_mode = EMIT_ALL_CONFIDENT_SITES
+ case "EMIT_ALL_SITES" => output_mode = EMIT_ALL_SITES
+ case "EMIT_VARIANTS_ONLY" => output_mode = EMIT_VARIANTS_ONLY
+ case e => logger.warn("output mode '" + e + "' does not exist")
}
+ }
- if (config("inputtype", default = "dna").asString == "rna") {
- dontUseSoftClippedBases = config("dontusesoftclippedbases", default = true)
- stand_call_conf = config("stand_call_conf", default = 5)
- stand_emit_conf = config("stand_emit_conf", default = 0)
- } else {
- dontUseSoftClippedBases = config("dontusesoftclippedbases", default = false)
- stand_call_conf = config("stand_call_conf", default = 5)
- stand_emit_conf = config("stand_emit_conf", default = 0)
- }
+ if (config("inputtype", default = "dna").asString == "rna") {
+ dontUseSoftClippedBases = config("dontusesoftclippedbases", default = true)
+ stand_call_conf = config("stand_call_conf", default = 5)
+ stand_emit_conf = config("stand_emit_conf", default = 0)
+ } else {
+ dontUseSoftClippedBases = config("dontusesoftclippedbases", default = false)
+ stand_call_conf = config("stand_call_conf", default = 5)
+ stand_emit_conf = config("stand_emit_conf", default = 0)
+ }
+
+ override def afterGraph {
+ super.afterGraph
if (bamOutput != null && nct.getOrElse(1) > 1) {
nct = Option(1)
logger.warn("BamOutput is on, nct/threads is forced to set on 1, this option is only for debug")
--
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