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biopet.biopet
Commits
bbaaa914
Commit
bbaaa914
authored
Oct 29, 2015
by
Peter van 't Hof
Browse files
Fixed intermediate files
parent
09fe4d50
Changes
1
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protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
View file @
bbaaa914
...
...
@@ -43,8 +43,12 @@ 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
)
lazy
val
useIndelRealigner
:
Boolean
=
config
(
"use_indel_realigner"
,
default
=
true
)
lazy
val
useBaseRecalibration
:
Boolean
=
config
(
"use_base_recalibration"
,
default
=
true
)
override
def
summarySettings
=
super
.
summarySettings
+
(
"use_indel_realigner"
->
useIndelRealigner
)
+
(
"use_base_recalibration"
->
useBaseRecalibration
)
/** Return true when baserecalibration is executed */
protected
def
doneBaseRecalibrator
:
Boolean
=
{
...
...
@@ -69,12 +73,16 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
}
}
override
def
summarySettings
=
super
.
summarySettings
+
(
"use_indel_realigner"
->
useIndelRealigner
)
lazy
val
useIndelRealigner
:
Boolean
=
config
(
"use_indel_realigner"
,
default
=
true
)
/** This methods will add double preprocess steps, with GATK indel realignment */
override
protected
def
addDoublePreProcess
(
input
:
List
[
File
],
isIntermediate
:
Boolean
=
false
)
:
Option
[
File
]
=
{
if
(
input
.
size
<=
1
)
super
.
addDoublePreProcess
(
input
)
else
super
.
addDoublePreProcess
(
input
,
isIntermediate
=
true
).
collect
{
else
super
.
addDoublePreProcess
(
input
,
isIntermediate
=
useIndelRealigner
).
collect
{
case
file
=>
config
(
"
use
_i
ndel
_r
ealigner
"
,
default
=
true
).
asBoolean
match
{
use
I
ndel
R
ealigner
match
{
case
true
=>
addIndelRealign
(
file
,
sampleDir
,
isIntermediate
=
false
)
case
false
=>
file
}
...
...
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