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biopet.biopet
Commits
dc856bfa
Commit
dc856bfa
authored
Mar 09, 2015
by
Peter van 't Hof
Browse files
Fix on intermeditaite files
parent
b9117b9d
Changes
1
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protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
View file @
dc856bfa
...
...
@@ -36,15 +36,21 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
/** Class will generate library jobs */
class
Library
(
libId
:
String
)
extends
super
.
Library
(
libId
)
{
val
useIndelRealigner
:
Boolean
=
config
(
"use_indel_realigner"
,
default
=
true
)
val
useBaseRecalibration
:
Boolean
=
config
(
"use_base_recalibration"
,
default
=
true
)
/** Return true when baserecalibration is executed */
protected
def
doneBaseRecalibrator
:
Boolean
=
{
val
br
=
new
BaseRecalibrator
(
qscript
)
useBaseRecalibration
&&
!
br
.
knownSites
.
isEmpty
}
/** This will adds preprocess steps, gatk indel realignment and base recalibration is included here */
override
def
preProcess
(
input
:
File
)
:
Option
[
File
]
=
{
val
useIndelRealigner
:
Boolean
=
config
(
"use_indel_realigner"
,
default
=
true
)
val
useBaseRecalibration
:
Boolean
=
config
(
"use_base_recalibration"
,
default
=
true
)
if
(!
useIndelRealigner
&&
!
useBaseRecalibration
)
None
if
(!
useIndelRealigner
&&
!
doneBaseRecalibrator
)
None
else
{
val
indelRealignFile
=
useIndelRealigner
match
{
case
true
=>
addIndelRealign
(
input
,
libDir
,
us
eBaseRecalibrat
ion
||
libraries
.
size
>
1
)
case
true
=>
addIndelRealign
(
input
,
libDir
,
don
eBaseRecalibrat
or
||
libraries
.
size
>
1
)
case
false
=>
input
}
...
...
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