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biopet.biopet
Commits
2c1fb614
Commit
2c1fb614
authored
Sep 26, 2016
by
Sander Bollen
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Warning message for #385
parent
6efe0956
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-2
toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+6
-2
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toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
View file @
2c1fb614
...
...
@@ -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
{
...
...
@@ -92,6 +92,10 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
}
else
inputVcf
if
(
enableScatter
)
{
val
doNotRemove
:
Boolean
=
config
(
"do_not_remove"
,
namespace
=
"variant_effect_predictor"
,
default
=
false
)
if
(
doNotRemove
)
{
logger
.
warn
(
"Chunking combined with do_not_remove possibly leads to mangled CSQ fields"
)
}
val
outputVcfFiles
=
BedRecordList
.
fromReference
(
referenceFasta
())
.
scatter
(
config
(
"bin_size"
,
default
=
50000000
))
.
allRecords
.
map
{
region
=>
...
...
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