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biopet.biopet
Commits
6f32526d
Commit
6f32526d
authored
Nov 18, 2016
by
Peter van 't Hof
Browse files
Merge branch 'fix-BIOPET-383' into 'develop'
Fix biopet 383 See merge request !473
parents
e07f79b0
3951e8b8
Changes
3
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
6f32526d
...
...
@@ -52,7 +52,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
/** Adds the library jobs */
final
def
addAndTrackJobs
()
:
Unit
=
{
if
(
nameRegex
.
findFirstIn
(
libId
)
==
None
)
if
(
nameRegex
.
findFirstIn
(
libId
)
.
isEmpty
)
Logging
.
addError
(
s
"Library '$libId' $nameError"
)
currentSample
=
Some
(
sampleId
)
currentLib
=
Some
(
libId
)
...
...
@@ -139,9 +139,13 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
*/
def
makeLibrary
(
id
:
String
)
:
Library
/** returns a set with library names */
/** returns a set with library names
or throws error when not found
*/
protected
def
libIds
:
Set
[
String
]
=
{
ConfigUtils
.
getMapFromPath
(
globalConfig
.
map
,
List
(
"samples"
,
sampleId
,
"libraries"
)).
getOrElse
(
Map
()).
keySet
val
ids
=
ConfigUtils
.
getMapFromPath
(
globalConfig
.
map
,
List
(
"samples"
,
sampleId
,
"libraries"
)).
getOrElse
(
Map
()).
keySet
if
(
ids
.
isEmpty
)
{
throw
new
IllegalStateException
(
s
"No libraries found in config for sample $sampleId"
)
}
ids
}
/** Name overules the one from qscript */
...
...
@@ -151,7 +155,7 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
/** Adds sample jobs */
final
def
addAndTrackJobs
()
:
Unit
=
{
if
(
nameRegex
.
findFirstIn
(
sampleId
)
==
None
)
if
(
nameRegex
.
findFirstIn
(
sampleId
)
.
isEmpty
)
Logging
.
addError
(
s
"Sample '$sampleId' $nameError"
)
currentSample
=
Some
(
sampleId
)
addJobs
()
...
...
biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/MultiSampleQScriptTest.scala
View file @
6f32526d
...
...
@@ -15,10 +15,9 @@
package
nl.lumc.sasc.biopet.core
import
java.io.File
import
nl.lumc.sasc.biopet.core.MultiSampleQScript.Gender
import
nl.lumc.sasc.biopet.core.extensions.Md5sum
import
nl.lumc.sasc.biopet.utils.
{
Logging
,
ConfigUtils
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
org.broadinstitute.gatk.queue.QScript
import
org.scalatest.Matchers
...
...
@@ -119,6 +118,11 @@ class MultiSampleQScriptTest extends TestNGSuite with Matchers {
"Dash (-) and underscore (_) are permitted."
}
@Test
def
testNoLibSample
()
:
Unit
=
{
an
[
IllegalStateException
]
shouldBe
thrownBy
(
MultiSampleQScriptTest
(
noLibSample
::
Nil
))
}
}
object
MultiSampleQScriptTest
{
...
...
@@ -153,10 +157,48 @@ object MultiSampleQScriptTest {
"lib1"
->
Map
(
"test"
->
"4-1"
)
))))
val
child
=
Map
(
"samples"
->
Map
(
"child"
->
Map
(
"tags"
->
Map
(
"gender"
->
"male"
,
"father"
->
"father"
,
"mother"
->
"mother"
))))
val
father
=
Map
(
"samples"
->
Map
(
"father"
->
Map
(
"tags"
->
Map
(
"gender"
->
"male"
))))
val
mother
=
Map
(
"samples"
->
Map
(
"mother"
->
Map
(
"tags"
->
Map
(
"gender"
->
"female"
))))
val
child
=
Map
(
"samples"
->
Map
(
"child"
->
Map
(
"tags"
->
Map
(
"gender"
->
"male"
,
"father"
->
"father"
,
"mother"
->
"mother"
),
"libraries"
->
Map
(
"lib1"
->
Map
(
"test"
->
"child-1"
)
)
)
)
)
val
father
=
Map
(
"samples"
->
Map
(
"father"
->
Map
(
"tags"
->
Map
(
"gender"
->
"male"
),
"libraries"
->
Map
(
"lib1"
->
Map
(
"test"
->
"father-1"
)
)
)
)
)
val
mother
=
Map
(
"samples"
->
Map
(
"mother"
->
Map
(
"tags"
->
Map
(
"gender"
->
"female"
),
"libraries"
->
Map
(
"lib1"
->
Map
(
"test"
->
"mother-1"
)
)
)
)
)
val
noLibSample
=
Map
(
"samples"
->
Map
(
"sample1"
->
Map
(
"tags"
->
Map
(
"gender"
->
"female"
)
)
)
)
def
apply
(
configs
:
List
[
Map
[
String
,
Any
]],
only
:
List
[
String
]
=
Nil
)
=
{
new
QScript
with
MultiSampleQScript
{
qscript
=>
...
...
mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
View file @
6f32526d
...
...
@@ -14,7 +14,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.mapping
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
...
...
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