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biopet.biopet
Commits
d43c8265
Commit
d43c8265
authored
Sep 27, 2016
by
Peter van 't Hof
Browse files
Merge branch 'warning-do-note-remove' into 'develop'
Warning do note remove See merge request !453
parents
8a710c02
66a08a19
Changes
1
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toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @
d43c8265
...
...
@@ -58,9 +58,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
lazy
val
enableScatter
:
Boolean
=
config
(
"enable_scatter"
,
default
=
{
val
ref
=
new
FastaSequenceFile
(
referenceFasta
(),
true
)
val
refLeng
h
t
=
ref
.
getSequenceDictionary
.
getReferenceLength
val
refLengt
h
=
ref
.
getSequenceDictionary
.
getReferenceLength
ref
.
close
()
refLeng
h
t
>
minScatterGenomeSize
refLengt
h
>
minScatterGenomeSize
})
def
sampleInfo
:
Map
[
String
,
Map
[
String
,
Any
]]
=
root
match
{
...
...
@@ -112,6 +112,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
runChunk
(
sv
.
out
,
chunkDir
,
chunkName
)
}
if
(
this
.
functions
.
filter
(
_
.
isInstanceOf
[
VepNormalizer
]).
exists
(
_
.
asInstanceOf
[
VepNormalizer
].
doNotRemove
))
logger
.
warn
(
"Chunking combined with do_not_remove possibly leads to mangled CSQ fields"
)
val
cv
=
new
CatVariants
(
this
)
cv
.
variant
=
outputVcfFiles
.
toList
cv
.
outputFile
=
outputVcf
...
...
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