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biopet.biopet
Commits
b4cb9bd0
Commit
b4cb9bd0
authored
Apr 05, 2017
by
Peter van 't Hof
Browse files
Fixing files
parent
fb25247e
Changes
1
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
b4cb9bd0
...
...
@@ -97,8 +97,8 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
lazy
val
usePrintReads
:
Boolean
=
if
(
useBaseRecalibration
)
config
(
"use_printreads"
,
default
=
true
)
else
false
lazy
val
useAnalyzeCovariates
:
Boolean
=
if
(
useBaseRecalibration
)
config
(
"use_analyze_covariates"
,
default
=
true
)
else
false
lazy
val
bqsrFile
:
Option
[
File
]
=
if
(
useBaseRecalibration
)
Some
(
createFile
(
"
.
baserecal"
))
else
None
lazy
val
bqsrAfterFile
:
Option
[
File
]
=
if
(
useAnalyzeCovariates
)
Some
(
createFile
(
"
.
baserecal.after"
))
else
None
lazy
val
bqsrFile
:
Option
[
File
]
=
if
(
useBaseRecalibration
)
Some
(
createFile
(
"baserecal"
))
else
None
lazy
val
bqsrAfterFile
:
Option
[
File
]
=
if
(
useAnalyzeCovariates
)
Some
(
createFile
(
"baserecal.after"
))
else
None
override
def
keepFinalBamfile
=
super
.
keepFinalBamfile
&&
!
useIndelRealigner
&&
!
useBaseRecalibration
...
...
@@ -149,14 +149,14 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
/** Adds base recalibration jobs */
def
addBaseRecalibrator
(
inputBam
:
File
,
dir
:
File
,
isIntermediate
:
Boolean
,
usePrintreads
:
Boolean
)
:
File
=
{
val
baseRecalibrator
=
BaseRecalibrator
(
qscript
,
inputBam
,
swapExt
(
dir
,
inputBam
,
".bam"
,
".baserecal"
))
val
baseRecalibrator
=
BaseRecalibrator
(
qscript
,
inputBam
,
bqsrFile
.
get
)
// at this point bqsrFile should exist
if
(
baseRecalibrator
.
knownSites
.
isEmpty
)
return
inputBam
add
(
baseRecalibrator
)
val
baseRecalibratorAfter
=
BaseRecalibrator
(
qscript
,
inputBam
,
swapExt
(
dir
,
inputBam
,
".bam"
,
".baserecal.after"
))
baseRecalibratorAfter
.
BQSR
=
Some
(
baseRecalibrator
.
out
)
if
(
useAnalyzeCovariates
)
{
val
baseRecalibratorAfter
=
BaseRecalibrator
(
qscript
,
inputBam
,
bqsrAfterFile
.
get
)
baseRecalibratorAfter
.
BQSR
=
bqsrFile
add
(
baseRecalibratorAfter
)
add
(
AnalyzeCovariates
(
qscript
,
baseRecalibrator
.
out
,
baseRecalibratorAfter
.
out
,
swapExt
(
dir
,
inputBam
,
".bam"
,
".baserecal.pdf"
)))
}
...
...
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