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biopet.biopet
Commits
175de69a
Commit
175de69a
authored
May 27, 2016
by
Peter van 't Hof
Browse files
Adding error on missing alleles
parent
dee3612b
Changes
2
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Inline
Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala
View file @
175de69a
...
...
@@ -20,6 +20,7 @@
package
nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import
nl.lumc.sasc.biopet.extensions.gatk
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config.Configurable
/** Allele mode for Haplotypecaller */
...
...
@@ -27,9 +28,11 @@ class HaplotypeCallerAllele(val root: Configurable) extends Variantcaller {
val
name
=
"haplotypecaller_allele"
protected
def
defaultPrio
=
5
val
alleles
:
File
=
config
(
"input_alleles"
)
def
biopetScript
()
{
val
hc
=
gatk
.
HaplotypeCaller
(
this
,
inputBams
.
values
.
toList
,
outputFile
)
hc
.
alleles
=
config
(
"input_
alleles
"
)
hc
.
alleles
=
Some
(
alleles
)
hc
.
genotyping_mode
=
Some
(
"GENOTYPE_GIVEN_ALLELES"
)
add
(
hc
)
}
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala
View file @
175de69a
...
...
@@ -27,9 +27,11 @@ class UnifiedGenotyperAllele(val root: Configurable) extends Variantcaller {
val
name
=
"unifiedgenotyper_allele"
protected
def
defaultPrio
=
9
val
alleles
:
File
=
config
(
"input_alleles"
)
def
biopetScript
()
{
val
ug
=
gatk
.
UnifiedGenotyper
(
this
,
inputBams
.
values
.
toList
,
outputFile
)
ug
.
alleles
=
config
(
"input_
alleles
"
)
ug
.
alleles
=
Some
(
alleles
)
ug
.
genotyping_mode
=
Some
(
"GENOTYPE_GIVEN_ALLELES"
)
add
(
ug
)
}
...
...
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