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biopet.biopet
Commits
9c5f43ad
Commit
9c5f43ad
authored
Mar 09, 2015
by
bow
Browse files
Fix errors caused by merging
parent
5db19c93
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
View file @
9c5f43ad
...
...
@@ -29,7 +29,7 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
// mpileup, varscan, fix_mpileup.py, binom_test.py, bgzip, tabix
private
def
mpileup
=
new
SamtoolsMpileup
(
wrapper
.
root
)
{
this
.
input
=
wrapper
.
input
this
.
input
=
List
(
wrapper
.
input
)
disableBaq
=
true
reference
=
config
(
"reference"
)
depth
=
Option
(
1000000
)
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
9c5f43ad
...
...
@@ -156,7 +156,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
add
(
baiLn
)
val
bamLn
=
Ln
(
qscript
,
oldBamFile
,
bamFile
.
get
)
bamLn
.
deps
:+=
baiLn
.
out
bamLn
.
deps
:+=
baiLn
.
out
put
add
(
bamLn
)
}
...
...
@@ -197,7 +197,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
add
(
baiLn
)
val
bamLn
=
Ln
(
qscript
,
input
.
head
,
bamFile
)
bamLn
.
deps
:+=
baiLn
.
out
bamLn
.
deps
:+=
baiLn
.
out
put
add
(
bamLn
)
Some
(
bamFile
)
}
else
{
...
...
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