Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
e2c9fe3a
Commit
e2c9fe3a
authored
May 06, 2016
by
Peter van 't Hof
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Correct tests
parent
605a588e
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
with
2 additions
and
2 deletions
+2
-2
toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+1
-1
toucan/src/test/scala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
...ala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
+1
-1
No files found.
toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @
e2c9fe3a
...
...
@@ -49,7 +49,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
lazy
val
minScatterGenomeSize
:
Long
=
config
(
"min_scatter_genome_size"
,
default
=
75000000
)
lazy
val
enableScatter
:
Boolean
=
config
(
"enable_scater"
,
default
=
{
lazy
val
enableScatter
:
Boolean
=
config
(
"enable_scat
t
er"
,
default
=
{
val
ref
=
new
FastaSequenceFile
(
referenceFasta
(),
true
)
val
refLenght
=
ref
.
getSequenceDictionary
.
getReferenceLength
ref
.
close
()
...
...
toucan/src/test/scala/nl/lumc/sasc/biopet/pipelines/toucan/ToucanTest.scala
View file @
e2c9fe3a
...
...
@@ -37,7 +37,7 @@ class ToucanTest extends TestNGSuite with Matchers {
@Test
def
testBinning
()
:
Unit
=
{
val
pipeline
=
initPipeline
(
ToucanTest
.
config
++
Map
(
"bin_size"
->
4000
))
val
pipeline
=
initPipeline
(
ToucanTest
.
config
++
Map
(
"bin_size"
->
4000
,
"min_scatter_genome_size"
->
1000
))
pipeline
.
inputVcf
=
new
File
(
ToucanTest
.
resourcePath
(
"/chrQ2.vcf.gz"
))
pipeline
.
script
()
...
...
Write
Preview
Markdown
is supported
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