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biopet.biopet
Commits
311c28ef
Commit
311c28ef
authored
May 09, 2016
by
Peter van 't Hof
Browse files
Merge branch 'fix-gvcfs-extract' into 'develop'
Fix gvcfs extract See merge request !389
parents
f963bb6e
d03ff5ff
Changes
4
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
View file @
311c28ef
...
...
@@ -106,16 +106,12 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
@Gather
(
enabled
=
false
)
private
var
outputIndex
:
File
=
_
@Output
@Gather
(
enabled
=
false
)
private
var
dbsnpIndex
:
File
=
_
override
def
beforeGraph
()
{
super
.
beforeGraph
()
deps
++=
variant
.
filter
(
orig
=>
orig
!=
null
&&
(!
orig
.
getName
.
endsWith
(
".list"
))).
map
(
orig
=>
VcfUtils
.
getVcfIndexFile
(
orig
))
if
(
out
!=
null
&&
!
org
.
broadinstitute
.
gatk
.
utils
.
io
.
IOUtils
.
isSpecialFile
(
out
))
outputIndex
=
VcfUtils
.
getVcfIndexFile
(
out
)
dbsnp
.
foreach
(
x
=>
d
bsnpIndex
=
VcfUtils
.
getVcfIndexFile
(
x
))
dbsnp
.
foreach
(
x
=>
d
eps
:+
=
VcfUtils
.
getVcfIndexFile
(
x
))
}
override
def
cmdLine
=
super
.
cmdLine
+
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
View file @
311c28ef
...
...
@@ -73,7 +73,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
/** Variantcallers requested by the config */
protected
val
configCallers
:
Set
[
String
]
=
config
(
"variantcallers"
)
protected
val
callers
:
List
[
Variantcaller
]
=
{
val
callers
:
List
[
Variantcaller
]
=
{
(
for
(
name
<-
configCallers
)
yield
{
if
(!
callersList
.
exists
(
_
.
name
==
name
))
Logging
.
addError
(
s
"variantcaller '$name' does not exist, possible to use: "
+
callersList
.
map
(
_
.
name
).
mkString
(
", "
))
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
View file @
311c28ef
...
...
@@ -13,14 +13,21 @@ class HaplotypeCallerGvcf(val root: Configurable) extends Variantcaller {
val
name
=
"haplotypecaller_gvcf"
protected
def
defaultPrio
=
5
/**
* Map of sample name -> gvcf. May be empty.
*/
protected
var
gVcfFiles
:
Map
[
String
,
File
]
=
Map
()
def
getGvcfs
=
gVcfFiles
def
biopetScript
()
{
val
gvcfFiles
=
for
((
sample
,
inputBam
)
<-
inputBams
)
yield
{
val
hc
=
gatk
.
HaplotypeCaller
.
gvcf
(
this
,
inputBam
,
new
File
(
outputDir
,
sample
+
".gvcf.vcf.gz"
))
add
(
hc
)
hc
.
out
sample
->
hc
.
out
}
val
genotypeGVCFs
=
gatk
.
GenotypeGVCFs
(
this
,
gvcfFiles
.
toList
,
outputFile
)
val
genotypeGVCFs
=
gatk
.
GenotypeGVCFs
(
this
,
gvcfFiles
.
values
.
toList
,
outputFile
)
add
(
genotypeGVCFs
)
}
}
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala
View file @
311c28ef
...
...
@@ -28,6 +28,9 @@ trait Variantcaller extends QScript with BiopetQScript with Reference {
var
namePrefix
:
String
=
_
/**
* Map of samplename -> (preprocessed) bam file
*/
var
inputBams
:
Map
[
String
,
File
]
=
_
def
init
()
=
{}
...
...
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