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biopet.biopet
Commits
95f8441a
Commit
95f8441a
authored
Jun 01, 2016
by
Peter van 't Hof
Browse files
fixed a config value
parent
bfdad518
Changes
1
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Inline
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
View file @
95f8441a
...
...
@@ -90,7 +90,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
/** Mode for emitting reference confidence scores */
@Argument
(
fullName
=
"emitRefConfidence"
,
shortName
=
"ERC"
,
doc
=
"Mode for emitting reference confidence scores"
,
required
=
false
,
exclusiveOf
=
""
,
validation
=
""
)
var
emitRefConfidence
:
String
=
_
var
emitRefConfidence
:
Option
[
String
]
=
config
(
"emitRefConfidence"
)
/** File to which assembled haplotypes should be written */
@Output
(
fullName
=
"bamOutput"
,
shortName
=
"bamout"
,
doc
=
"File to which assembled haplotypes should be written"
,
required
=
false
,
exclusiveOf
=
""
,
validation
=
""
)
...
...
@@ -525,7 +525,7 @@ object HaplotypeCaller {
def
gvcf
(
root
:
Configurable
,
inputFile
:
File
,
outputFile
:
File
)
:
HaplotypeCaller
=
{
val
hc
=
apply
(
root
,
List
(
inputFile
),
outputFile
)
hc
.
emitRefConfidence
=
"GVCF"
hc
.
emitRefConfidence
=
Some
(
"GVCF"
)
hc
.
variant_index_type
=
Some
(
"LINEAR"
)
hc
.
variant_index_parameter
=
Some
(
hc
.
config
(
"variant_index_parameter"
,
default
=
128000
).
asInt
)
hc
...
...
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