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biopet.biopet
Commits
42e2ffe3
Commit
42e2ffe3
authored
Apr 20, 2017
by
Peter van 't Hof
Committed by
GitHub
Apr 20, 2017
Browse files
Merge pull request #85 from biopet/fix-BIOPET-661
Fixed bam input
parents
7d179c4e
6d672983
Changes
1
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Inline
Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
42e2ffe3
...
...
@@ -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"
))
...
...
@@ -189,7 +187,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
Some
(
makeVariantcalling
(
multisample
=
false
,
sample
=
Some
(
sampleId
)))
}
else
None
override
def
keepMergedFiles
:
Boolean
=
config
(
"keep_merged_files"
,
default
=
!
useIndelRealigner
)
override
def
keepMergedFiles
:
Boolean
=
config
(
"keep_merged_files"
,
default
=
!
useIndelRealigner
||
(
libraries
.
size
==
1
)
)
lazy
val
useIndelRealigner
:
Boolean
=
config
(
"use_indel_realigner"
,
default
=
true
)
...
...
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