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biopet.biopet
Commits
819bada6
Commit
819bada6
authored
Dec 16, 2016
by
Peter van 't Hof
Browse files
Added output files to bamstats
parent
8654affb
Changes
1
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Inline
Side-by-side
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala
View file @
819bada6
...
...
@@ -3,10 +3,10 @@ package nl.lumc.sasc.biopet.extensions.tools
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFunction
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFunction
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Input
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Created by pjvanthof on 18/11/2016.
...
...
@@ -36,6 +36,9 @@ class BamStats(val root: Configurable) extends ToolCommandFunction with Referenc
}
}
@Output
private
var
outputFiles
:
List
[
File
]
=
Nil
def
bamstatsSummary
:
File
=
new
File
(
outputDir
,
"bamstats.summary.json"
)
def
flagstatSummaryFile
(
contig
:
Option
[
String
]
=
None
)
:
File
=
getOutputFile
(
"flagstats.summary.json"
,
contig
)
def
mappingQualityFile
(
contig
:
Option
[
String
]
=
None
)
:
File
=
getOutputFile
(
"mapping_quality.tsv"
,
contig
)
...
...
@@ -44,6 +47,10 @@ class BamStats(val root: Configurable) extends ToolCommandFunction with Referenc
override
def
beforeGraph
()
{
super
.
beforeGraph
()
deps
:+=
new
File
(
bamFile
.
getAbsolutePath
.
replaceAll
(
".bam$"
,
".bai"
))
outputFiles
:+=
bamstatsSummary
outputFiles
:+=
flagstatSummaryFile
()
outputFiles
:+=
mappingQualityFile
()
outputFiles
:+=
clipingFile
()
jobOutputFile
=
new
File
(
outputDir
,
".bamstats.out"
)
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
...
...
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