remove javacall

hrehrauer · hrehrauer · commit 115a2c631e30 · 2021-12-04T14:18:59.000+01:00
diff --git a/R/app-gatkRnaHaplotyper.R b/R/app-gatkRnaHaplotyper.R
@@ -42,7 +42,6 @@ ezMethodGatkRnaHaplotyper = function(input=NA, output=NA, param=NA){
     ezSystem('mv local.bam withRg.bam')
   }
 
-  gatk = paste(javaCall, "-jar", Sys.getenv("GATK_jar"))
   cmd = paste(gatkCall, "SplitNCigarReads", 
               "-R", genomeSeq,
               "-I", "withRg.bam",

Original file line number	Diff line number	Diff line change
`@@ -42,7 +42,6 @@ ezMethodGatkRnaHaplotyper = function(input=NA, output=NA, param=NA){`
`42`	`42`	`ezSystem('mv local.bam withRg.bam')`
`43`	`43`	`}`
`44`	`44`
`45`		`- gatk = paste(javaCall, "-jar", Sys.getenv("GATK_jar"))`
`46`	`45`	`cmd = paste(gatkCall, "SplitNCigarReads",`
`47`	`46`	`"-R", genomeSeq,`
`48`	`47`	`"-I", "withRg.bam",`