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biopet.biopet
Commits
62fef674
Commit
62fef674
authored
Apr 26, 2016
by
Peter van 't Hof
Browse files
Fix compile errors
parent
b9a543ec
Changes
1
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
View file @
62fef674
...
...
@@ -104,7 +104,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
indelRealigner
.
isIntermediate
=
isIntermediate
add
(
indelRealigner
)
indelRealigner
.
o
indelRealigner
.
o
ut
}
/** Adds base recalibration jobs */
...
...
@@ -116,18 +116,18 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
if
(
config
(
"use_analyze_covariates"
,
default
=
false
).
asBoolean
)
{
val
baseRecalibratorAfter
=
BaseRecalibrator
(
this
,
inputBam
,
swapExt
(
dir
,
inputBam
,
".bam"
,
".baserecal.after"
))
baseRecalibratorAfter
.
BQSR
=
baseRecalibrator
.
o
baseRecalibratorAfter
.
BQSR
=
baseRecalibrator
.
o
ut
add
(
baseRecalibratorAfter
)
add
(
AnalyzeCovariates
(
this
,
baseRecalibrator
.
o
,
baseRecalibratorAfter
.
o
,
swapExt
(
dir
,
inputBam
,
".bam"
,
".baserecal.pdf"
)))
add
(
AnalyzeCovariates
(
this
,
baseRecalibrator
.
o
ut
,
baseRecalibratorAfter
.
o
ut
,
swapExt
(
dir
,
inputBam
,
".bam"
,
".baserecal.pdf"
)))
}
val
printReads
=
PrintReads
(
this
,
inputBam
,
swapExt
(
dir
,
inputBam
,
".bam"
,
".baserecal.bam"
))
printReads
.
BQSR
=
baseRecalibrator
.
o
printReads
.
BQSR
=
baseRecalibrator
.
o
ut
printReads
.
isIntermediate
=
isIntermediate
add
(
printReads
)
printReads
.
o
printReads
.
o
ut
}
}
...
...
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