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
54c312c0
Commit
54c312c0
authored
Mar 28, 2017
by
Sander Bollen
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
set vs list
parent
bcd47977
Changes
1
Show whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
5 additions
and
5 deletions
+5
-5
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PedigreeQscript.scala
...main/scala/nl/lumc/sasc/biopet/core/PedigreeQscript.scala
+5
-5
No files found.
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/PedigreeQscript.scala
View file @
54c312c0
...
...
@@ -69,17 +69,17 @@ trait PedigreeQscript extends MultiSampleQScript { qscript: QScript =>
* @return
*/
def
pedSamplesFromConfig
()
:
List
[
PedSample
]
=
{
val
totalSampleIds
=
samples
.
values
.
map
(
_
.
sampleId
).
toList
val
withFam
=
samples
.
values
.
filter
(
_
.
family
.
isDefined
)
val
fathers
=
withFam
.
filter
(
_
.
father
.
isDefined
).
flatMap
(
_
.
father
)
val
mothers
=
withFam
.
filter
(
_
.
mother
.
isDefined
).
flatMap
(
_
.
mother
)
val
sampleIds
=
withFam
.
map
(
_
.
sampleId
).
toSet
val
fathers
=
withFam
.
flatMap
(
_
.
father
)
val
mothers
=
withFam
.
flatMap
(
_
.
mother
)
fathers
.
foreach
{
f
=>
if
(!
withFam
.
map
(
_
.
sampleId
).
toList
.
contains
(
f
))
{
if
(!
sampleIds
.
contains
(
f
))
{
Logging
.
addError
(
s
"Father $f does not exist in samples"
)
}
}
mothers
.
foreach
{
m
=>
if
(!
withFam
.
map
(
_
.
sampleId
).
toList
.
contains
(
m
))
{
if
(!
sampleIds
.
contains
(
m
))
{
Logging
.
addError
(
s
"Mother $m does not exist in samples"
)
}
}
...
...
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