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biopet.biopet
Commits
755b864d
Commit
755b864d
authored
Oct 29, 2015
by
Wai Yi Leung
Browse files
More style fixes
parent
8a15fe3c
Changes
2
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/Sambamba.scala
View file @
755b864d
...
...
@@ -19,7 +19,7 @@ import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
/** General Sambamba extension */
abstract
class
Sambamba
extends
BiopetCommandLineFunction
with
Version
{
override
def
defaultCoreMemory
=
2
.0
override
def
defaultCoreMemory
=
4
.0
override
def
defaultThreads
=
2
override
def
subPath
=
"sambamba"
::
super
.
subPath
...
...
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
755b864d
...
...
@@ -73,14 +73,13 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript with Sam
def
biopetScript
()
:
Unit
=
{
val
fastqFiles
:
List
[
File
]
=
bamFile
.
map
{
bamfile
=>
// // sambamba view -f bam -F "unmapped or mate_is_unmapped" <alnFile> > <extracted.bam>
// val samFilterUnmapped = new SambambaView(this)
// samFilterUnmapped.input = bamfile
// samFilterUnmapped.filter = Some("(unmapped or mate_is_unmapped) and not (secondary_alignment) and [XH] == null")
// samFilterUnmapped.output = new File(outputDir, s"$outputName.unmapped.bam")
// samFilterUnmapped.isIntermediate = false
// add(samFilterUnmapped)
// // sambamba view -f bam -F "unmapped or mate_is_unmapped" <alnFile> > <extracted.bam>
// val samFilterUnmapped = new SambambaView(this)
// samFilterUnmapped.input = bamfile
// samFilterUnmapped.filter = Some("(unmapped or mate_is_unmapped) and not (secondary_alignment) and [XH] == null")
// samFilterUnmapped.output = new File(outputDir, s"$outputName.unmapped.bam")
// samFilterUnmapped.isIntermediate = false
// add(samFilterUnmapped)
val
samtoolsViewSelectUnmapped
=
new
SamtoolsView
(
this
)
samtoolsViewSelectUnmapped
.
input
=
bamfile
...
...
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