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biopet.biopet
Commits
844ff098
Commit
844ff098
authored
Jul 27, 2015
by
Peter van 't Hof
Browse files
Added sv calling to shiva
parent
9ca827e9
Changes
3
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public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
View file @
844ff098
...
...
@@ -179,7 +179,7 @@ trait BastyTrait extends MultiSampleQScript {
snpsOnly
:
Boolean
=
false
)
:
FastaOutput
=
{
val
bastyGenerateFasta
=
new
BastyGenerateFasta
(
this
)
bastyGenerateFasta
.
outputName
=
if
(
outputName
!=
null
)
outputName
else
sampleName
bastyGenerateFasta
.
inputVcf
=
shiva
.
variant
c
alling
.
get
.
finalFile
bastyGenerateFasta
.
inputVcf
=
shiva
.
variant
C
alling
.
get
.
finalFile
if
(
shiva
.
samples
.
contains
(
sampleName
))
{
bastyGenerateFasta
.
bamFile
=
shiva
.
samples
(
sampleName
).
preProcessBam
.
get
}
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
View file @
844ff098
...
...
@@ -44,7 +44,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
protected
var
inputBams
:
Map
[
String
,
File
]
=
Map
()
protected
def
addBamFile
(
file
:
File
,
sampleId
:
Option
[
String
]
=
None
)
:
Unit
=
{
def
addBamFile
(
file
:
File
,
sampleId
:
Option
[
String
]
=
None
)
:
Unit
=
{
sampleId
match
{
case
Some
(
sample
)
=>
inputBams
+=
sample
->
file
case
_
if
!
file
.
exists
()
=>
throw
new
IllegalArgumentException
(
"Bam file does not exits: "
+
file
)
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
844ff098
...
...
@@ -270,13 +270,19 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
}
}
lazy
val
variant
c
alling
=
if
(
config
(
"multisample_variantcalling"
,
default
=
true
).
asBoolean
)
{
lazy
val
variant
C
alling
=
if
(
config
(
"multisample_variantcalling"
,
default
=
true
).
asBoolean
)
{
Some
(
makeVariantcalling
(
multisample
=
true
))
}
else
None
lazy
val
svCalling
=
if
(
config
(
"sv_calling"
,
default
=
false
).
asBoolean
)
{
val
svCalling
=
new
ShivaSvCalling
(
this
)
samples
.
foreach
(
x
=>
x
.
_2
.
preProcessBam
.
foreach
(
bam
=>
svCalling
.
addBamFile
(
bam
,
Some
(
x
.
_1
))))
Some
(
svCalling
)
}
else
None
/** This will add the mutisample variantcalling */
def
addMultiSampleJobs
()
:
Unit
=
{
variant
c
alling
.
foreach
(
vc
=>
{
variant
C
alling
.
foreach
(
vc
=>
{
vc
.
outputDir
=
new
File
(
outputDir
,
"variantcalling"
)
vc
.
inputBams
=
samples
.
flatMap
(
_
.
_2
.
preProcessBam
).
toList
vc
.
init
()
...
...
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