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

Unfortunately need to bump up memory needed for liftover to get Omni file sorted

This commit is contained in:
Eric Banks 2012-03-12 23:20:00 -04:00
parent 359090c4b7
commit 6e9b8559d8
1 changed files with 1 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
View File

@ -320,7 +320,7 @@ class GATKResourcesBundle extends QScript {
} }
class LiftOverPerl(@Input val in: File, @Output val out: File, @Input val chain: File, oldRef: Reference, newRef: Reference) extends CommandLineFunction { class LiftOverPerl(@Input val in: File, @Output val out: File, @Input val chain: File, oldRef: Reference, newRef: Reference) extends CommandLineFunction {
this.memoryLimit = 8 this.memoryLimit = 12
def commandLine = ("%s -vcf %s -chain %s -out %s " + def commandLine = ("%s -vcf %s -chain %s -out %s " +
"-gatk ./ -newRef %s -oldRef %s -tmp %s").format(liftOverPerl, in.getAbsolutePath, chain, "-gatk ./ -newRef %s -oldRef %s -tmp %s").format(liftOverPerl, in.getAbsolutePath, chain,
out.getAbsolutePath, newRef.file.replace(".fasta", ""), out.getAbsolutePath, newRef.file.replace(".fasta", ""),