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biopet.biopet
Commits
d2c7fc48
Commit
d2c7fc48
authored
Apr 20, 2017
by
pjvan_thof
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Fixed bam input
parent
7d179c4e
Changes
1
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
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d2c7fc48
...
...
@@ -105,8 +105,6 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
override
def
keepFinalBamfile
:
Boolean
=
super
.
keepFinalBamfile
&&
!
useIndelRealigner
&&
!
useBaseRecalibration
override
def
bamFile
:
Option
[
Mapping
#
File
]
=
mapping
.
map
(
_
.
mergedBamFile
)
override
def
preProcessBam
:
Option
[
Mapping
#
File
]
=
if
(
useIndelRealigner
&&
usePrintReads
&&
useBaseRecalibration
)
bamFile
.
map
(
swapExt
(
libDir
,
_
,
".bam"
,
".realign.baserecal.bam"
))
else
if
(
useIndelRealigner
)
bamFile
.
map
(
swapExt
(
libDir
,
_
,
".bam"
,
".realign.bam"
))
...
...
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