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
278c4384
Commit
278c4384
authored
Apr 11, 2016
by
Peter van 't Hof
Browse files
Style changes
parent
2738a59f
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @
278c4384
...
...
@@ -264,17 +264,16 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
def
summaryStats
:
Map
[
String
,
Any
]
=
{
if
(
statsText
)
{
val
statsFile
:
File
=
new
File
(
output
.
getAbsolutePath
+
"_summary.txt"
)
parseStatsFile
(
statsFile
)
}
else
{
Map
()
}
if
(
statsText
)
parseStatsFile
(
new
File
(
output
.
getAbsolutePath
+
"_summary.txt"
))
else
Map
()
}
def
parseStatsFile
(
file
:
File
)
:
Map
[
String
,
Any
]
=
{
val
contents
=
Source
.
fromFile
(
file
).
getLines
().
toList
val
headers
=
getHeadersFromStatsFile
(
contents
)
val
headers
=
contents
.
filter
(
x
=>
x
.
startsWith
(
"["
)
&&
x
.
endsWith
(
"]"
))
.
map
(
_
.
stripPrefix
(
"["
).
stripSuffix
(
"]"
))
headers
.
foldLeft
(
Map
.
empty
[
String
,
Any
])((
acc
,
x
)
=>
acc
+
(
x
.
replace
(
" "
,
"_"
)
->
getBlockFromStatsFile
(
contents
,
x
)))
}
...
...
public/biopet-tools-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilterTest.scala
View file @
278c4384
...
...
@@ -19,7 +19,7 @@ import java.io.File
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
DataProvider
,
Test
}
import
org.testng.annotations.
{
DataProvider
,
Test
}
/**
* Created by ahbbollen on 2-3-16.
...
...
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