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biopet.biopet
Commits
95e63289
Commit
95e63289
authored
Apr 24, 2017
by
pjvan_thof
Browse files
Removed indelrealignment from library level
parent
9c692ecf
Changes
1
Hide whitespace changes
Inline
Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
95e63289
...
...
@@ -74,7 +74,10 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
/** Sample specific settings */
override
def
summarySettings
:
Map
[
String
,
Any
]
=
super
.
summarySettings
++
Map
(
"single_sample_variantcalling"
->
variantcalling
.
isDefined
,
"use_indel_realigner"
->
useIndelRealigner
)
Map
(
"single_sample_variantcalling"
->
variantcalling
.
isDefined
,
"use_indel_realigner"
->
useIndelRealigner
)
/** Class to generate jobs for a library */
class
Library
(
libId
:
String
)
extends
super
.
Library
(
libId
)
{
...
...
@@ -84,7 +87,6 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
bqsrFile
.
map
(
"baserecal"
->
_
)
++
bqsrAfterFile
.
map
(
"baserecal_after"
->
_
)
lazy
val
useIndelRealigner
:
Boolean
=
config
(
"use_indel_realigner"
,
default
=
true
)
lazy
val
useBaseRecalibration
:
Boolean
=
{
val
c
:
Boolean
=
config
(
"use_base_recalibration"
,
default
=
true
)
val
br
=
new
BaseRecalibrator
(
qscript
)
...
...
@@ -97,18 +99,15 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
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
:
Boolean
=
super
.
keepFinalBamfile
&&
!
use
Indel
Reali
gner
&&
!
use
BaseRecalibration
override
def
keepFinalBamfile
:
Boolean
=
super
.
keepFinalBamfile
&&
!
use
Base
Re
c
ali
bration
&&
!
use
PrintReads
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"
))
else
if
(
usePrintReads
&&
useBaseRecalibration
)
bamFile
.
map
(
swapExt
(
libDir
,
_
,
".bam"
,
".baserecal.bam"
))
override
def
preProcessBam
:
Option
[
Mapping
#
File
]
=
if
(
usePrintReads
&&
useBaseRecalibration
)
bamFile
.
map
(
swapExt
(
libDir
,
_
,
".bam"
,
".baserecal.bam"
))
else
bamFile
/** Library specific settings */
override
def
summarySettings
:
Map
[
String
,
Any
]
=
super
.
summarySettings
++
Map
(
"library_variantcalling"
->
variantcalling
.
isDefined
,
"use_indel_realigner"
->
useIndelRealigner
,
"use_base_recalibration"
->
useBaseRecalibration
,
"useAnalyze_covariates"
->
useAnalyzeCovariates
)
...
...
@@ -122,12 +121,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
override
def
addJobs
()
:
Unit
=
{
super
.
addJobs
()
if
(
useIndelRealigner
&&
useBaseRecalibration
)
{
val
file
=
addIndelRealign
(
bamFile
.
get
,
libDir
,
isIntermediate
=
true
)
addBaseRecalibrator
(
file
,
libDir
,
libraries
.
size
>
1
,
usePrintReads
)
}
else
if
(
useIndelRealigner
)
{
addIndelRealign
(
bamFile
.
get
,
libDir
,
libraries
.
size
>
1
)
}
else
if
(
useBaseRecalibration
)
{
if
(
useBaseRecalibration
)
{
addBaseRecalibrator
(
bamFile
.
get
,
libDir
,
libraries
.
size
>
1
,
usePrintReads
)
}
...
...
@@ -195,7 +189,7 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
override
def
addJobs
()
:
Unit
=
{
super
.
addJobs
()
if
(
useIndelRealigner
&&
libraries
.
values
.
flatMap
(
_
.
preProcessBam
).
size
>
1
)
{
if
(
useIndelRealigner
)
{
addIndelRealign
(
bamFile
.
get
,
sampleDir
,
isIntermediate
=
false
)
}
...
...
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