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biopet.biopet
Commits
adc39c81
Commit
adc39c81
authored
Nov 18, 2016
by
Peter van 't Hof
Browse files
Add basic version of bamstats to pipeline
parent
6f32526d
Changes
2
Hide whitespace changes
Inline
Side-by-side
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
adc39c81
...
...
@@ -16,13 +16,13 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import
java.io.File
import
nl.lumc.sasc.biopet.core.annotations.
{
AnnotationRefFlat
,
RibosomalRefFlat
}
import
nl.lumc.sasc.biopet.core.annotations.
{
AnnotationRefFlat
,
RibosomalRefFlat
}
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
BiopetFifoPipe
,
PipelineCommand
,
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
,
BedtoolsSort
}
import
nl.lumc.sasc.biopet.core.
{
BiopetFifoPipe
,
PipelineCommand
,
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.bedtools.
{
BedtoolsCoverage
,
BedtoolsIntersect
,
BedtoolsSort
}
import
nl.lumc.sasc.biopet.extensions.picard._
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
import
nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
import
nl.lumc.sasc.biopet.extensions.tools.
{
BamStats
,
BiopetFlagstat
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.intervals.BedCheck
...
...
@@ -86,6 +86,11 @@ class BamMetrics(val root: Configurable) extends QScript
add
(
biopetFlagstat
)
addSummarizable
(
biopetFlagstat
,
"biopet_flagstat"
)
val
bamStats
=
new
BamStats
(
this
)
bamStats
.
bamFile
=
inputBam
bamStats
.
outputDir
=
new
File
(
outputDir
,
"bamstats"
)
add
(
bamStats
)
val
multiMetrics
=
new
CollectMultipleMetrics
(
this
)
multiMetrics
.
input
=
inputBam
multiMetrics
.
outputName
=
new
File
(
outputDir
,
inputBam
.
getName
.
stripSuffix
(
".bam"
))
...
...
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala
0 → 100644
View file @
adc39c81
package
nl.lumc.sasc.biopet.extensions.tools
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFunction
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Input
/**
* Created by pjvanthof on 18/11/2016.
*/
class
BamStats
(
val
root
:
Configurable
)
extends
ToolCommandFunction
with
Reference
{
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
bamstats
.
BamStats
@Input
(
required
=
true
)
var
reference
:
File
=
_
@Input
(
required
=
true
)
var
bamFile
:
File
=
_
var
outputDir
:
File
=
_
var
binSize
:
Option
[
Int
]
=
config
(
"bin_size"
)
var
threadBinSize
:
Option
[
Int
]
=
config
(
"thread_bin_size"
)
override
def
defaultThreads
=
3
override
def
defaultCoreMemory
=
5.0
/** Creates command to execute extension */
override
def
cmdLine
=
super
.
cmdLine
+
required
(
"-b"
,
bamFile
)
+
required
(
"-o"
,
outputDir
)
+
required
(
"-R"
,
reference
)
+
optional
(
"--binSize"
,
binSize
),
optional
(
"--threadBinSize"
,
threadBinSize
)
}
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