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biopet.biopet
Commits
e66c1eec
Commit
e66c1eec
authored
Apr 17, 2017
by
Peter van 't Hof
Committed by
GitHub
Apr 17, 2017
Browse files
Merge pull request #77 from biopet/revert-69-fix-BIOPET-654
Revert "Remove default arguments"
parents
9c66f418
8ba7938f
Changes
1
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Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
View file @
e66c1eec
...
...
@@ -60,6 +60,11 @@ 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
{
if
(
genderAwareCalling
)
{
...
...
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