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biopet.biopet
Commits
dd458aef
Commit
dd458aef
authored
Jun 29, 2016
by
Wai Yi Leung
Browse files
Update code with fixes from Peter
parent
afe2bbcb
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/WipeReads.scala
View file @
dd458aef
...
...
@@ -42,7 +42,7 @@ 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
=
tru
e
)
var
limitRemoval
:
Boolean
=
config
(
"limit_removal"
,
default
=
fals
e
)
@Argument
(
doc
=
"Whether to index output BAM file or not"
)
var
noMakeIndex
:
Boolean
=
config
(
"no_make_index"
,
default
=
false
)
...
...
@@ -59,9 +59,17 @@ class WipeReads(val root: Configurable) extends ToolCommandFunction {
@Output
(
doc
=
"Output BAM"
,
shortName
=
"o"
,
required
=
true
)
var
outputBam
:
File
=
null
@Output
(
required
=
false
)
private
var
outputIndex
:
Option
[
File
]
=
None
@Output
(
doc
=
"BAM containing discarded reads"
,
shortName
=
"f"
,
required
=
false
)
var
discardedBam
:
Option
[
File
]
=
None
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(!
noMakeIndex
)
outputIndex
=
Some
(
new
File
(
outputBam
.
getPath
.
stripSuffix
(
".bam"
)
+
".bai"
))
}
override
def
cmdLine
=
super
.
cmdLine
+
required
(
"-I"
,
inputBam
)
+
required
(
"-r"
,
intervalFile
)
+
...
...
gentrap/src/test/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapTest.scala
View file @
dd458aef
...
...
@@ -138,9 +138,8 @@ abstract class GentrapTestAbstract(val expressionMeasure: String, val aligner: O
assert
(
gentrap
.
functions
.
exists
(
_
.
isInstanceOf
[
Ln
]))
}
if
(
gentrap
.
removeRibosomalReads
)
{
assert
(
gentrap
.
functions
.
exists
(
_
.
isInstanceOf
[
WipeReads
]))
}
gentrap
.
removeRibosomalReads
shouldBe
removeRiboReads
gentrap
.
functions
.
exists
(
_
.
isInstanceOf
[
WipeReads
])
shouldBe
removeRiboReads
val
classMap
=
Map
(
"gsnap"
->
classOf
[
Gsnap
],
...
...
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