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biopet.biopet
Commits
e5e47f6c
Commit
e5e47f6c
authored
Aug 17, 2016
by
Peter van 't Hof
Browse files
Fix default 0
parent
cdc1f3c6
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @
e5e47f6c
...
...
@@ -275,8 +275,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
else
Map
()
}
protected
val
removeOnConflict
=
Set
(
"Output_file"
,
"Run_time"
,
"Start_time"
,
"End_time"
,
"Novel_/_existing_variants"
)
protected
val
nonNumber
=
Set
(
"VEP_version_(API)"
,
"Cache/Database"
,
"Species"
,
"Command_line_options"
,
"Input_file_(format)"
)
protected
val
removeOnConflict
=
Set
(
"Output_file"
,
"Run_time"
,
"Start_time"
,
"End_time"
,
"Novel_/_existing_variants"
,
"Input_file_(format)"
)
protected
val
nonNumber
=
Set
(
"VEP_version_(API)"
,
"Cache/Database"
,
"Species"
,
"Command_line_options"
)
override
def
resolveSummaryConflict
(
v1
:
Any
,
v2
:
Any
,
key
:
String
)
:
Any
=
{
if
(
removeOnConflict
.
contains
(
key
))
None
...
...
@@ -303,7 +303,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
val
name
=
header
.
stripPrefix
(
"["
).
stripSuffix
(
"]"
)
name
.
replaceAll
(
" "
,
"_"
)
->
(
contents
.
drop
(
headerIndex
+
1
).
takeWhile
(!
isHeader
(
_
)).
map
{
line
=>
val
values
=
line
.
split
(
"\t"
,
2
)
values
.
head
.
replaceAll
(
" "
,
"_"
)
->
tryToParseNumber
(
values
.
last
).
getOrElse
(
0
)
values
.
head
.
replaceAll
(
" "
,
"_"
)
->
tryToParseNumber
(
values
.
last
).
getOrElse
(
values
.
last
)
}.
toMap
)
}).
toMap
}
...
...
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