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biopet.biopet
Commits
4f24e9f3
Commit
4f24e9f3
authored
Aug 22, 2014
by
Peter van 't Hof
Browse files
Remove old functions
parent
3decab94
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
4f24e9f3
...
...
@@ -228,36 +228,6 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
outputFiles
+=
(
"finalBamFile"
->
bamFile
)
}
// def addSortSam(inputSam: List[File], outputFile: File, dir: String): File = {
// val sortSam = new SortSam
// sortSam.input = inputSam
// sortSam.createIndex = true
// sortSam.output = outputFile
// sortSam.memoryLimit = 2
// sortSam.nCoresRequest = 2
// sortSam.jobResourceRequests :+= "h_vmem=4G"
// if (!skipMarkduplicates) sortSam.isIntermediate = true
// add(sortSam)
//
// return sortSam.output
// }
// def addMergeBam(inputSam: List[File], outputFile: File, dir: String): File = {
// val mergeSam = new MergeSamFiles
// mergeSam.input = inputSam
// mergeSam.createIndex = true
// mergeSam.output = outputFile
// mergeSam.memoryLimit = 2
// mergeSam.nCoresRequest = 2
// mergeSam.assumeSorted = true
// mergeSam.USE_THREADING = true
// mergeSam.jobResourceRequests :+= "h_vmem=4G"
// if (!skipMarkduplicates) mergeSam.isIntermediate = true
// add(mergeSam)
//
// return mergeSam.output
// }
def
addAddOrReplaceReadGroups
(
inputSam
:
File
,
outputDir
:
String
)
:
File
=
{
val
addOrReplaceReadGroups
=
AddOrReplaceReadGroups
(
this
,
inputSam
,
outputDir
)
addOrReplaceReadGroups
.
createIndex
=
true
...
...
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