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biopet.biopet
Commits
eb40009e
Commit
eb40009e
authored
Dec 15, 2016
by
Peter van 't Hof
Browse files
Fixing stackoverflow
parent
c882c5ac
Changes
2
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Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
View file @
eb40009e
...
...
@@ -101,12 +101,13 @@ trait MultisampleMappingTrait extends MultiSampleQScript
lazy
val
bamToFastq
:
Boolean
=
config
(
"bam_to_fastq"
,
default
=
false
)
lazy
val
correctReadgroups
:
Boolean
=
config
(
"correct_readgroups"
,
default
=
false
)
def
keepFinalBamfile
=
samples
(
sampleId
).
libraries
.
size
==
1
lazy
val
mapping
:
Option
[
Mapping
]
=
if
(
inputR1
.
isDefined
||
(
inputBam
.
isDefined
&&
bamToFastq
))
{
val
m
:
Mapping
=
new
Mapping
(
qscript
)
{
override
def
configNamespace
=
"mapping"
override
def
defaults
:
Map
[
String
,
Any
]
=
super
.
defaults
++
Map
(
"keep_final_bamfile"
->
!(
samples
(
lib
.
sampleId
).
libraries
.
size
>
1
||
preProcessBam
.
map
(
_
!=
bamFile
).
getOrElse
(
false
)))
Map
(
"keep_final_bamfile"
->
keepFinalBamfile
)
}
m
.
sampleId
=
Some
(
sampleId
)
m
.
libId
=
Some
(
libId
)
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
eb40009e
...
...
@@ -86,6 +86,8 @@ class Shiva(val root: Configurable) extends QScript with MultisampleMappingTrait
c
&&
br
.
knownSites
.
nonEmpty
}
override
def
keepFinalBamfile
=
super
.
keepFinalBamfile
&&
!
useIndelRealigner
&&
!
useBaseRecalibration
override
def
preProcessBam
=
if
(
useIndelRealigner
&&
useBaseRecalibration
)
bamFile
.
map
(
swapExt
(
libDir
,
_
,
".bam"
,
".realign.baserecal.bam"
))
else
if
(
useIndelRealigner
)
bamFile
.
map
(
swapExt
(
libDir
,
_
,
".bam"
,
".realign.bam"
))
...
...
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