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biopet.biopet
Commits
0211653b
Commit
0211653b
authored
Apr 16, 2017
by
Peter van 't Hof
Committed by
GitHub
Apr 16, 2017
Browse files
Revert "Remove default arguments"
parent
811fe4c2
Changes
1
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Inline
Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
View file @
0211653b
...
...
@@ -36,6 +36,11 @@ class HaplotypeCallerGvcf(val parent: Configurable) extends Variantcaller {
override
def
fixedValues
=
Map
(
"haplotypecaller"
->
Map
(
"emitRefConfidence"
->
"GVCF"
))
override
def
defaults
=
Map
(
"haplotypecaller"
->
Map
(
"variant_index_type"
->
"LINEAR"
,
"variant_index_parameter"
->
128000
)
)
def
biopetScript
()
{
gVcfFiles
=
for
((
sample
,
inputBam
)
<-
inputBams
)
yield
{
val
hc
=
gatk
.
HaplotypeCaller
(
this
,
List
(
inputBam
),
new
File
(
outputDir
,
sample
+
".gvcf.vcf.gz"
))
...
...
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