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biopet.biopet
Commits
9d86b1ed
Commit
9d86b1ed
authored
Mar 12, 2015
by
Sander Bollen
Browse files
Fix BamMetrics to use file in stead of directory
Fix markduplicates to not overwrite bam file with metrics file
parent
0267b656
Changes
3
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public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
9d86b1ed
...
...
@@ -88,8 +88,9 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
for
(
bedFile
<-
bedFiles
)
{
//TODO: Add target jobs to summary
val
targetDir
=
new
File
(
outputDir
,
bedFile
.
getName
.
stripSuffix
(
".bed"
))
val
targetInterval
=
BedToInterval
(
this
,
bedFile
,
inputBam
,
targetDir
)
val
targetDir
=
bedFile
.
getParentFile
val
targetFile
=
new
File
(
outputDir
,
bedFile
.
getName
.
stripSuffix
(
".bed"
)
+
".interval"
)
val
targetInterval
=
BedToInterval
(
this
,
bedFile
,
inputBam
,
targetFile
)
add
(
targetInterval
,
true
)
add
(
CalculateHsMetrics
(
this
,
inputBam
,
if
(
baitIntervalFile
!=
null
)
baitIntervalFile
else
targetInterval
.
output
,
targetInterval
.
output
,
targetDir
))
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
View file @
9d86b1ed
...
...
@@ -43,14 +43,6 @@ class BedToInterval(val root: Configurable) extends BiopetJavaCommandLineFunctio
}
object
BedToInterval
extends
ToolCommand
{
def
apply
(
root
:
Configurable
,
inputBed
:
File
,
inputBam
:
File
,
outputDir
:
String
)
:
BedToInterval
=
{
val
bedToInterval
=
new
BedToInterval
(
root
)
bedToInterval
.
input
=
inputBed
bedToInterval
.
bamFile
=
inputBam
bedToInterval
.
output
=
new
File
(
outputDir
,
inputBed
.
getName
.
stripSuffix
(
".bed"
)
+
".interval"
)
return
bedToInterval
}
def
apply
(
root
:
Configurable
,
inputBed
:
File
,
inputBam
:
File
,
output
:
File
)
:
BedToInterval
=
{
val
bedToInterval
=
new
BedToInterval
(
root
)
bedToInterval
.
input
=
inputBed
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
9d86b1ed
...
...
@@ -219,7 +219,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
val
md
=
new
MarkDuplicates
(
qscript
)
md
.
input
=
input
md
.
output
=
new
File
(
sampleDir
,
sampleId
+
".dedup.bam"
)
md
.
outputMetrics
=
new
File
(
sampleDir
,
sampleId
+
".dedup.
bam
"
)
md
.
outputMetrics
=
new
File
(
sampleDir
,
sampleId
+
".dedup.
metrics
"
)
md
.
isIntermediate
=
isIntermediate
add
(
md
)
addSummarizable
(
md
,
"mark_duplicates"
)
...
...
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