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biopet.biopet
Commits
51f0b19d
Commit
51f0b19d
authored
Jan 22, 2017
by
Peter van 't Hof
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Fixing code warnings
parent
6fc498a4
Changes
2
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2 changed files
with
6 additions
and
5 deletions
+6
-5
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+5
-5
biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/UtilsTest.scala
.../src/test/scala/nl/lumc/sasc/biopet/utils/UtilsTest.scala
+1
-0
No files found.
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @
51f0b19d
...
...
@@ -40,10 +40,10 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var
vepScript
:
String
=
config
(
"vep_script"
)
@Input
(
doc
=
"input VCF"
,
required
=
true
)
var
input
:
File
=
null
var
input
:
File
=
_
@Output
(
doc
=
"output file"
,
required
=
true
)
var
output
:
File
=
null
var
output
:
File
=
_
override
def
subPath
=
{
if
(
vepVersion
.
isSet
)
super
.
subPath
++
List
(
"vep_settings"
)
++
vepVersion
()
...
...
@@ -160,7 +160,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
override
def
defaultCoreMemory
=
4.0
@Output
private
var
_summary
:
File
=
null
private
var
_summary
:
File
=
_
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
...
...
@@ -312,11 +312,11 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
(
for
((
header
,
headerIndex
)
<-
headers
)
yield
{
val
name
=
header
.
stripPrefix
(
"["
).
stripSuffix
(
"]"
)
name
.
replaceAll
(
" "
,
"_"
)
->
(
contents
.
drop
(
headerIndex
+
1
).
takeWhile
(!
isHeader
(
_
)).
flatMap
{
line
=>
name
.
replaceAll
(
" "
,
"_"
)
->
contents
.
drop
(
headerIndex
+
1
).
takeWhile
(!
isHeader
(
_
)).
flatMap
{
line
=>
val
values
=
line
.
split
(
"\t"
,
2
)
if
(
values
.
last
.
isEmpty
||
values
.
last
==
"-"
)
None
else
Some
(
values
.
head
.
replaceAll
(
" "
,
"_"
)
->
tryToParseNumber
(
values
.
last
).
getOrElse
(
values
.
last
))
}.
toMap
)
}.
toMap
}).
toMap
}
}
biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/UtilsTest.scala
View file @
51f0b19d
...
...
@@ -6,6 +6,7 @@ import org.testng.annotations.Test
/**
* Created by Sander Bollen on 12-10-16.
* Here we test utils
*/
class
UtilsTest
extends
TestNGSuite
with
Matchers
{
...
...
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