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biopet.biopet
Commits
e86f6183
Commit
e86f6183
authored
Feb 17, 2015
by
bow
Browse files
Fix cryptic pipeline errors caused by using directory as output files
parent
9a5a8577
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
View file @
e86f6183
...
...
@@ -30,17 +30,11 @@ class SamtoolsFlagstat(val root: Configurable) extends Samtools {
}
object
SamtoolsFlagstat
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
)
:
SamtoolsFlagstat
=
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
Dir
:
File
)
:
SamtoolsFlagstat
=
{
val
flagstat
=
new
SamtoolsFlagstat
(
root
)
flagstat
.
input
=
input
flagstat
.
output
=
output
return
flagstat
}
def
apply
(
root
:
Configurable
,
input
:
File
,
outputDir
:
String
)
:
SamtoolsFlagstat
=
{
val
dir
=
if
(
outputDir
.
endsWith
(
"/"
))
outputDir
else
outputDir
+
"/"
val
outputFile
=
new
File
(
dir
+
swapExtension
(
input
.
getName
))
return
apply
(
root
,
input
,
outputFile
)
flagstat
.
output
=
new
File
(
outputDir
+
swapExtension
(
input
.
getName
))
flagstat
}
def
apply
(
root
:
Configurable
,
input
:
File
)
:
SamtoolsFlagstat
=
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
View file @
e86f6183
...
...
@@ -40,17 +40,11 @@ class BiopetFlagstat(val root: Configurable) extends BiopetJavaCommandLineFuncti
}
object
BiopetFlagstat
extends
ToolCommand
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
)
:
BiopetFlagstat
=
{
val
flagstat
=
new
BiopetFlagstat
(
root
)
flagstat
.
input
=
input
flagstat
.
output
=
output
return
flagstat
}
def
apply
(
root
:
Configurable
,
input
:
File
,
outputDir
:
String
)
:
BiopetFlagstat
=
{
def
apply
(
root
:
Configurable
,
input
:
File
,
outputDir
:
File
)
:
BiopetFlagstat
=
{
val
flagstat
=
new
BiopetFlagstat
(
root
)
flagstat
.
input
=
input
flagstat
.
output
=
new
File
(
outputDir
,
input
.
getName
.
stripSuffix
(
".bam"
)
+
".biopetflagstat"
)
return
flagstat
flagstat
}
case
class
Args
(
inputFile
:
File
=
null
,
region
:
Option
[
String
]
=
None
)
extends
AbstractArgs
...
...
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