zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added a temporary gatkLoggingLevel field to the soon to be obsolete GatkFunction while finishing up the delayed generic gatk walker utility. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3757 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2010-07-11 03:27:32 +00:00
parent c3c66e853c
commit 1d399aa2f3
2 changed files with 8 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
scala/qscript/unifiedgenotyper_example.properties
View File

@ -4,3 +4,4 @@ dbsnp = /path/to/dbsnp
intervals = /path/to/my.interval_list
jobNamePrefix = Q
memoryLimit = 2
gatkLoggingLevel = INFO

9
scala/src/org/broadinstitute/sting/queue/function/gatk/GatkFunction.scala
View File

@ -4,6 +4,7 @@ import java.io.File
import org.broadinstitute.sting.queue.function.IntervalFunction
import org.broadinstitute.sting.queue.function.scattergather.{Scatter, ScatterGatherableFunction, IntervalScatterFunction}
import org.broadinstitute.sting.commandline.{ClassType, Input}
import org.apache.log4j.Level
trait GatkFunction extends ScatterGatherableFunction with IntervalFunction {
@Input(doc="Temporary directory to write any files", required=false)
@ -26,8 +27,12 @@ trait GatkFunction extends ScatterGatherableFunction with IntervalFunction {
@Input(doc="DBSNP", required=false)
var dbsnp: File = _
@Input(doc="Logging level", required=false)
var gatkLoggingLevel: String = _
protected def gatkCommandLine(walker: String) =
"java%s%s -jar %s -T %s -R %s%s%s%s "
"java%s%s -jar %s -T %s -R %s%s%s%s%s "
.format(optional(" -Xmx", memoryLimit, "g"), optional(" -Djava.io.tmpdir=", javaTmpDir),
gatkJar, walker, referenceFile, repeat(" -I ", bamFiles), optional(" -D ", dbsnp), optional(" -L ", intervals))
gatkJar, walker, referenceFile, repeat(" -I ", bamFiles), optional(" -l ", gatkLoggingLevel),
optional(" -D ", dbsnp), optional(" -L ", intervals))
}