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biopet.biopet
Commits
85e5d3c1
Commit
85e5d3c1
authored
Apr 04, 2017
by
Sander Bollen
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bddec662
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tarmac/src/main/scala/nl/lumc/sasc/biopet/pipelines/tarmac/Tarmac.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/tarmac/Tarmac.scala
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tarmac/src/main/scala/nl/lumc/sasc/biopet/pipelines/tarmac/Tarmac.scala
View file @
85e5d3c1
...
...
@@ -52,6 +52,9 @@ class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with
val
outFile
=
new
File
(
sampleDir
+
File
.
separator
+
s
"$name.dcov"
)
(
inputXhmmCountFile
,
bamFile
)
match
{
case
(
Some
(
f
),
_
)
=>
{
if
(
bamFile
.
isDefined
)
{
logger
.
warn
(
s
"Both BAM and Xhmm count files are given for sample $name. The BAM file will be ignored"
)
}
val
ln
=
new
Ln
(
root
)
ln
.
input
=
f
ln
.
output
=
outFile
...
...
@@ -86,6 +89,9 @@ class Tarmac(val parent: Configurable) extends QScript with PedigreeQscript with
val
outFile
=
new
File
(
sampleDir
+
File
.
separator
+
s
"$name.wisecondor.bed"
)
(
inputWisecondorCountFile
,
bamFile
)
match
{
case
(
Some
(
f
),
_
)
=>
{
if
(
bamFile
.
isDefined
)
{
logger
.
warn
(
s
"Both BAM and Wisecondor count files are given for sample $name. The BAM file will be ignored"
)
}
val
ln
=
new
Ln
(
root
)
ln
.
input
=
f
ln
.
output
=
outFile
...
...
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