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biopet.biopet
Commits
531c04b7
Commit
531c04b7
authored
Nov 09, 2016
by
Sander Bollen
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Merge branch 'fix-delly' into 'develop'
Sortvcf on the end See merge request !468
parents
7ccf5ce0
85da3de4
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20 additions
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28 deletions
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-28
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
...nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
+19
-27
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
...lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
+1
-1
No files found.
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
View file @
531c04b7
...
...
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import
nl.lumc.sasc.biopet.extensions.delly.DellyCaller
import
nl.lumc.sasc.biopet.extensions.gatk.CatVariants
import
nl.lumc.sasc.biopet.extensions.picard.SortVcf
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config.Configurable
/** Script for sv caller delly */
...
...
@@ -33,69 +34,60 @@ 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"
)
catVariants
.
isIntermediate
=
true
if
(
del
)
{
val
delly
=
new
DellyCaller
(
this
)
delly
.
input
=
bamFile
delly
.
analysistype
=
"DEL"
delly
.
isIntermediate
=
true
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
"${sample}.delly.del.vcf.gz"
)
add
(
compressedVCF
)
catVariants
.
variant
:+=
compressedVCF
.
output
catVariants
.
variant
:+=
delly
.
outputvcf
}
if
(
dup
)
{
val
delly
=
new
DellyCaller
(
this
)
delly
.
input
=
bamFile
delly
.
analysistype
=
"DUP"
delly
.
isIntermediate
=
true
delly
.
outputvcf
=
new
File
(
dellyDir
,
sample
+
".delly.dup.vcf"
)
add
(
delly
)
val
compressedVCF
=
new
SortVcf
(
this
)
compressedVCF
.
input
=
delly
.
outputvcf
compressedVCF
.
output
=
new
File
(
dellyDir
,
s
"${sample}.delly.dup.vcf.gz"
)
add
(
compressedVCF
)
catVariants
.
variant
:+=
compressedVCF
.
output
catVariants
.
variant
:+=
delly
.
outputvcf
}
if
(
inv
)
{
val
delly
=
new
DellyCaller
(
this
)
delly
.
input
=
bamFile
delly
.
analysistype
=
"INV"
delly
.
isIntermediate
=
true
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
"${sample}.delly.inv.vcf.gz"
)
add
(
compressedVCF
)
catVariants
.
variant
:+=
compressedVCF
.
output
catVariants
.
variant
:+=
delly
.
outputvcf
}
if
(
tra
)
{
val
delly
=
new
DellyCaller
(
this
)
delly
.
input
=
bamFile
delly
.
analysistype
=
"TRA"
delly
.
isIntermediate
=
true
delly
.
outputvcf
=
new
File
(
dellyDir
,
sample
+
".delly.tra.vcf"
)
add
(
delly
)
val
compressedVCF
=
new
SortVcf
(
this
)
compressedVCF
.
input
=
delly
.
outputvcf
compressedVCF
.
output
=
new
File
(
dellyDir
,
s
"${sample}.delly.tra.vcf.gz"
)
add
(
compressedVCF
)
catVariants
.
variant
:+=
compressedVCF
.
output
catVariants
.
variant
:+=
delly
.
outputvcf
}
require
(
catVariants
.
variant
.
non
Empty
,
"At least 1 SV-type should be selected for Delly"
)
if
(
catVariants
.
variant
.
is
Empty
)
Logging
.
addError
(
"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
.
outputFile
+
".gz"
add
(
compressedVCF
)
addVCF
(
sample
,
compressedVCF
.
output
)
}
}
}
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingTest.scala
View file @
531c04b7
...
...
@@ -130,7 +130,7 @@ class ShivaSvCallingTest extends TestNGSuite with Matchers {
pipeline
.
inputBams
=
Map
(
"bam"
->
ShivaSvCallingTest
.
inputTouch
(
"bam"
+
".bam"
))
if
(!
del
&&
!
dup
&&
!
inv
&&
!
tra
)
intercept
[
Illegal
Argument
Exception
]
{
if
(!
del
&&
!
dup
&&
!
inv
&&
!
tra
)
intercept
[
Illegal
State
Exception
]
{
pipeline
.
init
()
pipeline
.
script
()
}
...
...
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