Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
8b40a367
Commit
8b40a367
authored
Jun 29, 2016
by
Wai Yi Leung
Browse files
Style fix
parent
dd458aef
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
View file @
8b40a367
...
...
@@ -42,10 +42,10 @@ class WipeReads(val root: Configurable) extends ToolCommandFunction {
var
readgroup
:
Set
[
String
]
=
config
(
"read_group"
,
default
=
Nil
)
@Argument
(
doc
=
"Whether to remove multiple-mapped reads outside the target regions (default: yes)"
)
var
limitRemoval
:
Boolean
=
config
(
"limit_removal"
,
default
=
false
)
var
limitRemoval
:
Boolean
=
config
(
"limit_removal"
,
default
=
false
)
@Argument
(
doc
=
"Whether to index output BAM file or not"
)
var
noMakeIndex
:
Boolean
=
config
(
"no_make_index"
,
default
=
false
)
var
noMakeIndex
:
Boolean
=
config
(
"no_make_index"
,
default
=
false
)
@Argument
(
doc
=
"GTF feature containing intervals (default: exon)"
)
var
featureType
:
Option
[
String
]
=
config
(
"feature_type"
)
...
...
@@ -67,7 +67,7 @@ class WipeReads(val root: Configurable) extends ToolCommandFunction {
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(!
noMakeIndex
)
outputIndex
=
Some
(
new
File
(
outputBam
.
getPath
.
stripSuffix
(
".bam"
)
+
".bai"
))
if
(!
noMakeIndex
)
outputIndex
=
Some
(
new
File
(
outputBam
.
getPath
.
stripSuffix
(
".bam"
)
+
".bai"
))
}
override
def
cmdLine
=
super
.
cmdLine
+
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment