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Just cleaning up 

clean up old commented code from tha data processing pipeline.
This commit is contained in:
Mauricio Carneiro 2011-09-07 13:31:20 -04:00
parent 743bf7784c
commit ee9d599558
1 changed files with 0 additions and 23 deletions
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23
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -37,11 +37,6 @@ class DataProcessingPipeline extends QScript {
* Optional Parameters * Optional Parameters
****************************************************************************/ ****************************************************************************/
// @Input(doc="path to Picard's SortSam.jar (if re-aligning a previously processed BAM file)", fullName="path_to_sort_jar", shortName="sort", required=false)
// var sortSamJar: File = _
//
@Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false) @Input(doc="extra VCF files to use as reference indels for Indel Realignment", fullName="extra_indels", shortName="indels", required=false)
var indels: List[File] = List() var indels: List[File] = List()
@ -132,24 +127,6 @@ class DataProcessingPipeline extends QScript {
} }
} }
return sampleTable.toMap return sampleTable.toMap
// println("\n\n*** INPUT FILES ***\n")
// // Creating one file for each sample in the dataset
// val sampleBamFiles = scala.collection.mutable.Map.empty[String, File]
// for ((sample, flist) <- sampleTable) {
//
// println(sample + ":")
// for (f <- flist)
// println (f)
// println()
//
// val sampleFileName = new File(qscript.outputDir + qscript.projectName + "." + sample + ".list")
// sampleBamFiles(sample) = sampleFileName
// //add(writeList(flist, sampleFileName))
// }
// println("*** INPUT FILES ***\n\n")
//
// return sampleBamFiles.toMap
} }
// Rebuilds the Read Group string to give BWA // Rebuilds the Read Group string to give BWA