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biopet.biopet
Commits
8506c344
Commit
8506c344
authored
Mar 09, 2015
by
Peter van 't Hof
Browse files
Config name change
parent
fea40cc0
Changes
2
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protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
View file @
8506c344
...
...
@@ -38,7 +38,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
/** This will adds preprocess steps, gatk indel realignment and base recalibration is included here */
override
def
preProcess
(
input
:
File
)
:
Option
[
File
]
=
{
val
useIndelRealigner
:
Boolean
=
config
(
"use_indel_realign"
,
default
=
true
)
val
useIndelRealigner
:
Boolean
=
config
(
"use_indel_realign
er
"
,
default
=
true
)
val
useBaseRecalibration
:
Boolean
=
config
(
"use_base_recalibration"
,
default
=
true
)
if
(!
useIndelRealigner
&&
!
useBaseRecalibration
)
None
...
...
@@ -61,7 +61,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
if
(
input
.
size
<=
1
)
super
.
addDoublePreProcess
(
input
)
else
super
.
addDoublePreProcess
(
input
,
true
).
collect
{
case
file
=>
{
config
(
"use_indel_realign"
,
default
=
true
).
asBoolean
match
{
config
(
"use_indel_realign
er
"
,
default
=
true
).
asBoolean
match
{
case
true
=>
addIndelRealign
(
file
,
sampleDir
,
false
)
case
false
=>
file
}
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
View file @
8506c344
...
...
@@ -48,7 +48,9 @@ class ShivaTest extends TestNGSuite with Matchers {
ConfigUtils
.
mergeMaps
(
Map
(
"multisample_sample_variantcalling"
->
multi
,
"single_sample_variantcalling"
->
single
,
"library_variantcalling"
->
library
,
"use_analyze_covariates"
->
covariates
,
"use_indel_realign"
->
realign
,
"use_base_recalibration"
->
baseRecalibration
),
m
.
toMap
)
"use_analyze_covariates"
->
covariates
,
"use_indel_realigner"
->
realign
,
"use_base_recalibration"
->
baseRecalibration
),
m
.
toMap
)
}
...
...
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