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biopet.biopet
Commits
7f1ff523
Commit
7f1ff523
authored
Feb 16, 2015
by
Peter van 't Hof
Browse files
Fix outputDirs
parent
28b42baf
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
7f1ff523
...
...
@@ -50,8 +50,8 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
}
def
biopetScript
()
{
add
(
SamtoolsFlagstat
(
this
,
inputBam
,
outputDir
))
add
(
BiopetFlagstat
(
this
,
inputBam
,
outputDir
))
add
(
SamtoolsFlagstat
(
this
,
inputBam
,
swapExt
(
outputDir
,
inputBam
,
".bam"
,
".flagstat"
)
))
add
(
BiopetFlagstat
(
this
,
inputBam
,
swapExt
(
outputDir
,
inputBam
,
".bam"
,
".biopetflagstat"
)
))
add
(
CollectGcBiasMetrics
(
this
,
inputBam
,
outputDir
))
add
(
CollectInsertSizeMetrics
(
this
,
inputBam
,
outputDir
))
add
(
CollectAlignmentSummaryMetrics
(
this
,
inputBam
,
outputDir
))
...
...
@@ -69,13 +69,13 @@ class BamMetrics(val root: Configurable) extends QScript with BiopetQScript {
val
strictOutputBam
=
new
File
(
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".overlap.strict.bam"
)
add
(
BedtoolsIntersect
(
this
,
inputBam
,
bedFile
,
strictOutputBam
,
minOverlap
=
config
(
"strictintersectoverlap"
,
default
=
1.0
)),
true
)
add
(
SamtoolsFlagstat
(
this
,
strictOutputBam
))
add
(
BiopetFlagstat
(
this
,
strictOutputBam
,
targetDir
))
add
(
SamtoolsFlagstat
(
this
,
strictOutputBam
,
swapExt
(
targetDir
,
strictOutputBam
,
".bam"
,
".flagstat"
)
))
add
(
BiopetFlagstat
(
this
,
strictOutputBam
,
swapExt
(
targetDir
,
strictOutputBam
,
".bam"
,
".biopetflagstat"
)
))
val
looseOutputBam
=
new
File
(
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".overlap.loose.bam"
)
add
(
BedtoolsIntersect
(
this
,
inputBam
,
bedFile
,
looseOutputBam
,
minOverlap
=
config
(
"looseintersectoverlap"
,
default
=
0.01
)),
true
)
add
(
SamtoolsFlagstat
(
this
,
looseOutputBam
))
add
(
BiopetFlagstat
(
this
,
looseOutputBam
,
targetDir
))
add
(
SamtoolsFlagstat
(
this
,
looseOutputBam
,
swapExt
(
targetDir
,
looseOutputBam
,
".bam"
,
".biopet"
)
))
add
(
BiopetFlagstat
(
this
,
looseOutputBam
,
swapExt
(
targetDir
,
looseOutputBam
,
".bam"
,
".biopetflagstat"
)
))
val
coverageFile
=
new
File
(
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".coverage"
)
add
(
BedtoolsCoverage
(
this
,
inputBam
,
bedFile
,
coverageFile
,
true
),
true
)
...
...
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