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biopet.biopet
Commits
7f03f1ef
Commit
7f03f1ef
authored
Apr 10, 2017
by
Peter van 't Hof
Browse files
Fixing null pointer
parent
78159ed9
Changes
2
Hide whitespace changes
Inline
Side-by-side
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
7f03f1ef
...
...
@@ -154,7 +154,6 @@ class BamMetrics(val parent: Configurable) extends QScript
val
biStrict
=
BedtoolsIntersect
(
this
,
inputBam
,
intervals
.
bed
,
output
=
new
File
(
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".overlap.strict.sam"
),
minOverlap
=
config
(
"strict_intersect_overlap"
,
default
=
1.0
))
biStrict
.
jobOutputFile
=
new
File
(
targetDir
,
".biStrict.Bedtools.out"
)
val
biopetFlagstatStrict
=
BiopetFlagstat
(
this
,
biStrict
.
output
,
targetDir
)
addSummarizable
(
biopetFlagstatStrict
,
targetName
+
"_flagstats_strict"
)
add
(
new
BiopetFifoPipe
(
this
,
List
(
biStrict
,
biopetFlagstatStrict
)))
...
...
@@ -162,7 +161,6 @@ class BamMetrics(val parent: Configurable) extends QScript
val
biLoose
=
BedtoolsIntersect
(
this
,
inputBam
,
intervals
.
bed
,
output
=
new
File
(
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".overlap.loose.sam"
),
minOverlap
=
config
(
"loose_intersect_overlap"
,
default
=
0.01
))
biLoose
.
jobOutputFile
=
new
File
(
targetDir
,
".biLoose.Bedtools.out"
)
val
biopetFlagstatLoose
=
BiopetFlagstat
(
this
,
biLoose
.
output
,
targetDir
)
addSummarizable
(
biopetFlagstatLoose
,
targetName
+
"_flagstats_loose"
)
add
(
new
BiopetFifoPipe
(
this
,
List
(
biLoose
,
biopetFlagstatLoose
)))
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
7f03f1ef
...
...
@@ -99,7 +99,7 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
beforeGraph
()
internalBeforeGraph
()
this
.
commandDirectory
=
this
.
jobOutputFile
.
getParentFile
if
(
jobOutputFile
!=
null
)
this
.
commandDirectory
=
this
.
jobOutputFile
.
getAbsoluteFile
.
getParentFile
super
.
freezeFieldValues
()
}
...
...
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