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biopet.biopet
Commits
abb1f25e
Commit
abb1f25e
authored
Oct 25, 2016
by
Peter van 't Hof
Browse files
For for BIOPET-389
parent
e6199e01
Changes
1
Hide whitespace changes
Inline
Side-by-side
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
abb1f25e
...
...
@@ -166,11 +166,15 @@ class BamMetrics(val root: Configurable) extends QScript
addSummarizable
(
biopetFlagstatLoose
,
targetName
+
"_biopet_flagstat_loose"
)
add
(
new
BiopetFifoPipe
(
this
,
List
(
biLoose
,
biopetFlagstatLoose
)))
val
sorter
=
new
BedtoolsSort
(
this
)
sorter
.
input
=
intervals
.
bed
sorter
.
output
=
swapExt
(
targetDir
,
intervals
.
bed
,
".bed"
,
".sorted.bed"
)
add
(
sorter
)
val
bedCov
=
BedtoolsCoverage
(
this
,
sorter
.
output
,
inputBam
,
depth
=
true
)
val
sortedBed
=
BamMetrics
.
sortedbedCache
.
getOrElse
(
intervals
.
bed
,
{
val
sorter
=
new
BedtoolsSort
(
this
)
sorter
.
input
=
intervals
.
bed
sorter
.
output
=
swapExt
(
targetDir
,
intervals
.
bed
,
".bed"
,
".sorted.bed"
)
add
(
sorter
)
BamMetrics
.
sortedbedCache
+=
intervals
.
bed
->
sorter
.
output
sorter
.
output
})
val
bedCov
=
BedtoolsCoverage
(
this
,
sortedBed
,
inputBam
,
depth
=
true
)
val
covStats
=
CoverageStats
(
this
,
targetDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
)
+
".coverage"
)
covStats
.
title
=
Some
(
"Coverage Plot"
)
covStats
.
subTitle
=
Some
(
s
"for file '$targetName.bed'"
)
...
...
@@ -198,4 +202,6 @@ object BamMetrics extends PipelineCommand {
bamMetrics
.
biopetScript
()
bamMetrics
}
private
var
sortedbedCache
:
Map
[
File
,
File
]
=
Map
()
}
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