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biopet.biopet
Commits
e6ed0297
Commit
e6ed0297
authored
Jan 18, 2017
by
Sander Bollen
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harmonize summary keys for flagstats
parent
31be1177
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1
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bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+2
-2
No files found.
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
e6ed0297
...
...
@@ -158,14 +158,14 @@ class BamMetrics(val root: Configurable) extends QScript
output
=
new
File
(
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".overlap.strict.sam"
),
minOverlap
=
config
(
"strict_intersect_overlap"
,
default
=
1.0
))
val
biopetFlagstatStrict
=
BiopetFlagstat
(
this
,
biStrict
.
output
,
targetDir
)
addSummarizable
(
biopetFlagstatStrict
,
targetName
+
"_
biopet_
flagstat_strict"
)
addSummarizable
(
biopetFlagstatStrict
,
targetName
+
"_flagstat
s
_strict"
)
add
(
new
BiopetFifoPipe
(
this
,
List
(
biStrict
,
biopetFlagstatStrict
)))
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
))
val
biopetFlagstatLoose
=
BiopetFlagstat
(
this
,
biLoose
.
output
,
targetDir
)
addSummarizable
(
biopetFlagstatLoose
,
targetName
+
"_
biopet_
flagstat_loose"
)
addSummarizable
(
biopetFlagstatLoose
,
targetName
+
"_flagstat
s
_loose"
)
add
(
new
BiopetFifoPipe
(
this
,
List
(
biLoose
,
biopetFlagstatLoose
)))
val
sortedBed
=
BamMetrics
.
sortedbedCache
.
getOrElse
(
intervals
.
bed
,
{
...
...
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