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biopet.biopet
Commits
d0a06da2
Commit
d0a06da2
authored
Nov 04, 2016
by
Peter van 't Hof
Browse files
Sortvcf on the end
parent
57b31904
Changes
1
Hide whitespace changes
Inline
Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
View file @
d0a06da2
...
...
@@ -33,7 +33,7 @@ class Delly(val root: Configurable) extends SvCaller {
val
dellyDir
=
new
File
(
outputDir
,
sample
)
val
catVariants
=
new
CatVariants
(
this
)
catVariants
.
outputFile
=
new
File
(
dellyDir
,
sample
+
".delly.vcf
.gz
"
)
catVariants
.
outputFile
=
new
File
(
dellyDir
,
sample
+
".delly.vcf"
)
if
(
del
)
{
val
delly
=
new
DellyCaller
(
this
)
...
...
@@ -42,12 +42,7 @@ class Delly(val root: Configurable) extends SvCaller {
delly
.
outputvcf
=
new
File
(
dellyDir
,
sample
+
".delly.del.vcf"
)
add
(
delly
)
val
compressedVCF
=
new
SortVcf
(
this
)
compressedVCF
.
input
=
delly
.
outputvcf
compressedVCF
.
output
=
new
File
(
dellyDir
,
s
"${sample}.delly.del.vcf.gz"
)
add
(
compressedVCF
)
catVariants
.
variant
:+=
compressedVCF
.
output
catVariants
.
variant
:+=
delly
.
outputvcf
}
if
(
dup
)
{
val
delly
=
new
DellyCaller
(
this
)
...
...
@@ -56,12 +51,7 @@ class Delly(val root: Configurable) extends SvCaller {
delly
.
outputvcf
=
new
File
(
dellyDir
,
sample
+
".delly.dup.vcf"
)
add
(
delly
)
val
compressedVCF
=
new
SortVcf
(
this
)
compressedVCF
.
input
=
delly
.
outputvcf
compressedVCF
.
output
=
new
File
(
dellyDir
,
s
"${sample}.delly.dup.vcf.gz"
)
add
(
compressedVCF
)
catVariants
.
variant
:+=
compressedVCF
.
output
catVariants
.
variant
:+=
delly
.
outputvcf
}
if
(
inv
)
{
val
delly
=
new
DellyCaller
(
this
)
...
...
@@ -70,12 +60,7 @@ class Delly(val root: Configurable) extends SvCaller {
delly
.
outputvcf
=
new
File
(
dellyDir
,
sample
+
".delly.inv.vcf"
)
add
(
delly
)
val
compressedVCF
=
new
SortVcf
(
this
)
compressedVCF
.
input
=
delly
.
outputvcf
compressedVCF
.
output
=
new
File
(
dellyDir
,
s
"${sample}.delly.inv.vcf.gz"
)
add
(
compressedVCF
)
catVariants
.
variant
:+=
compressedVCF
.
output
catVariants
.
variant
:+=
delly
.
outputvcf
}
if
(
tra
)
{
val
delly
=
new
DellyCaller
(
this
)
...
...
@@ -84,18 +69,19 @@ class Delly(val root: Configurable) extends SvCaller {
delly
.
outputvcf
=
new
File
(
dellyDir
,
sample
+
".delly.tra.vcf"
)
add
(
delly
)
val
compressedVCF
=
new
SortVcf
(
this
)
compressedVCF
.
input
=
delly
.
outputvcf
compressedVCF
.
output
=
new
File
(
dellyDir
,
s
"${sample}.delly.tra.vcf.gz"
)
add
(
compressedVCF
)
catVariants
.
variant
:+=
compressedVCF
.
output
catVariants
.
variant
:+=
delly
.
outputvcf
}
require
(
catVariants
.
variant
.
nonEmpty
,
"At least 1 SV-type should be selected for Delly"
)
add
(
catVariants
)
addVCF
(
sample
,
catVariants
.
outputFile
)
val
compressedVCF
=
new
SortVcf
(
this
)
compressedVCF
.
input
=
catVariants
.
outputFile
compressedVCF
.
output
=
catVariants
+
".gz"
add
(
compressedVCF
)
addVCF
(
sample
,
compressedVCF
.
output
)
}
}
}
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