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Commented out changes to ADPR and VariantEval modules that are causing this script to not compile. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4353 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2010-09-25 15:12:10 +00:00
parent 70f03a7113
commit 9bfbc3b784
1 changed files with 28 additions and 24 deletions
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52
scala/qscript/fullCallingPipeline.q
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@ -179,12 +179,15 @@ class fullCallingPipeline extends QScript {
.toList
// actually make calls
endToEnd(uncleanedBase,recalibratedBamFiles, adprRscript, seq, expKind)
//endToEnd(uncleanedBase,recalibratedBamFiles, adprRscript, seq, expKind)
endToEnd(uncleanedBase,recalibratedBamFiles, seq, expKind)
// COMMENT THIS NEXT LINE TO AVOID CALLING ON CLEANED FILES
endToEnd(cleanedBase,cleanBamFiles, adprRscript, seq, expKind)
//endToEnd(cleanedBase,cleanBamFiles, adprRscript, seq, expKind)
endToEnd(cleanedBase,cleanBamFiles, seq, expKind)
}
def endToEnd(base: String, bamFiles: List[File], adprthing: File, seqinfo: String, exptype: String) = {
//def endToEnd(base: String, bamFiles: List[File], adprthing: File, seqinfo: String, exptype: String) = {
def endToEnd(base: String, bamFiles: List[File], seqinfo: String, exptype: String) = {
// step through the un-indel-cleaned graph:
// 1a. call snps and indels
@ -319,32 +322,32 @@ class fullCallingPipeline extends QScript {
eval.rodBind :+= RodBind("evalOptimized", "VCF", cut.out)
eval.rodBind :+= RodBind("evalHandFiltered", "VCF", handFilter.out)
eval.evalModule ++= List("CountFunctionalClasses", "CompOverlap", "CountVariants", "TiTvVariantEvaluator")
eval.reportLocation = new File(base+".eval")
eval.reportType = "R"
//eval.reportLocation = new File(base+".eval")
//eval.reportType = "R"
eval.analysisName = base+"_VariantEval"
add(snps)
// 5. Run the ADPR and make pretty stuff
val adpr = new CommandLineFunction{
@Input(doc="Dependent files") var dependents: File = _
@Output(doc="Automated Data processing report") var out: File = _
var setname: String
var protocol: String
var sequencer: String
var scriptloc: File
def commandLine = "Rscript %s %s %s %s"
.format(scriptloc, setname, protocol, sequencer)
}
adpr.setname = base
adpr.scriptloc = adprthing
adpr.sequencer = seqinfo
adpr.protocol = exptype
adpr.dependents = eval.reportLocation
adpr.out = new File(base + "_adpr.pdf")
adpr.analysisName = base + "_ADPR"
// val adpr = new CommandLineFunction{
// @Input(doc="Dependent files") var dependents: File = _
// @Output(doc="Automated Data processing report") var out: File = _
// var setname: String
// var protocol: String
// var sequencer: String
// var scriptloc: File
// def commandLine = "Rscript %s %s %s %s"
// .format(scriptloc, setname, protocol, sequencer)
// }
//
// adpr.setname = base
// adpr.scriptloc = adprthing
// adpr.sequencer = seqinfo
// adpr.protocol = exptype
// adpr.dependents = eval.reportLocation
// adpr.out = new File(base + "_adpr.pdf")
// adpr.analysisName = base + "_ADPR"
//In order for ADPR to finish successfully, a squid file for both the lane and sample level data needs to be
// produced, reformatted and named <projectBase>_lanes.txt or <projectBase>_samps.txt, respectively. These files
// to be in the working directory. When database access is ready, this and the protocol and sequencer parameters of
@ -355,7 +358,8 @@ class fullCallingPipeline extends QScript {
add(igv2)
}
add(mergeIndels,annotated,masker,handFilter,clusters,recalibrate,cut,eval,adpr)
// add(mergeIndels,annotated,masker,handFilter,clusters,recalibrate,cut,eval,adpr)
add(mergeIndels,annotated,masker,handFilter,clusters,recalibrate,cut,eval)
}