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biopet.biopet
Commits
b43464ed
Commit
b43464ed
authored
Apr 06, 2017
by
Peter van 't Hof
Browse files
Give a warning in de logwhen a variantcaller is used that does not support this.
parent
06a147a3
Changes
1
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
b43464ed
...
...
@@ -245,6 +245,14 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
if
(!
usePrintReads
)
vc
.
inputBqsrFiles
=
samples
.
flatMap
{
case
(
sampleId
,
sample
)
=>
sample
.
bqsrFile
.
map
(
sampleId
->
_
)
}
add
(
vc
)
if
(!
usePrintReads
)
{
import
variantcallers._
if
(
vc
.
callers
.
exists
(
_
match
{
case
_:
HaplotypeCaller
|
_
:HaplotypeCallerAllele
|
_
:HaplotypeCallerGvcf
=>
false
case
_:
UnifiedGenotyper
|
_
:UnifiedGenotyperAllele
=>
false
case
_
=>
true
}))
logger
.
warn
(
"Not all variantcallers chosen can read BQSR files, All non-GATK"
)
}
annotation
.
foreach
{
toucan
=>
toucan
.
outputDir
=
new
File
(
outputDir
,
"annotation"
)
...
...
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