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biopet.biopet
Commits
ad20fbd3
Commit
ad20fbd3
authored
Feb 03, 2017
by
Peter van 't Hof
Browse files
Format issues
parent
90e81770
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
View file @
ad20fbd3
...
...
@@ -514,9 +514,9 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
conditional
(
filter_bases_not_stored
,
"-filterNoBases"
,
escape
=
true
,
format
=
"%s"
)
+
(
this
.
getVersion
match
{
case
Some
(
s
)
if
s
.
contains
(
"3.0"
)
|
s
.
contains
(
"3.1"
)
|
s
.
contains
(
"3.2"
)
|
s
.
contains
(
"3.3"
)
|
s
.
contains
(
"3.4"
)
|
s
.
contains
(
"3.5"
)
|
s
.
contains
(
"3.6"
)
=>
optional
(
"-stand_emit_conf"
,
standard_min_confidence_threshold_for_emitting
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
standard_min_confidence_threshold_for_emittingFormat
)
optional
(
"-stand_emit_conf"
,
standard_min_confidence_threshold_for_emitting
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
standard_min_confidence_threshold_for_emittingFormat
)
case
_
=>
""
})
})
}
object
HaplotypeCaller
{
...
...
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