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biopet.biopet
Commits
95b665ed
Commit
95b665ed
authored
Oct 06, 2015
by
Sander van der Zeeuw
Browse files
added mapping qual filter to Carp
parent
e32722e8
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-extentsions/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsView.scala
View file @
95b665ed
...
...
@@ -28,7 +28,7 @@ class SamtoolsView(val root: Configurable) extends Samtools {
@Output
(
doc
=
"output File"
)
var
output
:
File
=
null
var
q
uality
:
Option
[
Int
]
=
config
(
"q
uality
"
)
var
q
:
Option
[
Int
]
=
config
(
"q"
)
var
b
:
Boolean
=
config
(
"b"
,
default
=
false
)
var
h
:
Boolean
=
config
(
"h"
,
default
=
false
)
var
f
:
List
[
String
]
=
config
(
"f"
,
default
=
List
.
empty
[
String
])
...
...
@@ -36,7 +36,7 @@ class SamtoolsView(val root: Configurable) extends Samtools {
def
cmdBase
=
required
(
executable
)
+
required
(
"view"
)
+
optional
(
"-q"
,
q
uality
)
+
optional
(
"-q"
,
q
)
+
repeat
(
"-f"
,
f
)
+
repeat
(
"-F"
,
F
)
+
conditional
(
b
,
"-b"
)
+
...
...
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
95b665ed
...
...
@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.carp
import
java.io.File
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import
nl.lumc.sasc.biopet.utils.config._
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.extensions.Ln
...
...
@@ -40,11 +41,14 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
override
def
defaults
=
ConfigUtils
.
mergeMaps
(
Map
(
"mapping"
->
Map
(
"skip_markduplicates"
->
tru
e
,
"skip_markduplicates"
->
fals
e
,
"aligner"
->
"bwa-mem"
)
),
"samtoolsview"
->
Map
(
"q"
->
10
)
),
super
.
defaults
)
def
summaryFile
=
new
File
(
outputDir
,
"Carp.summary.json"
)
//TODO: Add summary
...
...
@@ -93,6 +97,7 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
}
val
bamFile
=
createFile
(
".bam"
)
val
bamFileFilter
=
createFile
(
".filter.bam"
)
val
controls
:
List
[
String
]
=
config
(
"control"
,
default
=
Nil
)
def
addJobs
()
:
Unit
=
{
...
...
@@ -116,8 +121,15 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
addSummaryQScript
(
bamMetrics
)
addAll
(
Bam2Wig
(
qscript
,
bamFile
).
functions
)
val
samtoolsView
=
new
SamtoolsView
(
qscript
)
samtoolsView
.
input
=
bamFile
samtoolsView
.
output
=
bamFileFilter
samtoolsView
.
b
=
true
samtoolsView
.
h
=
true
add
(
samtoolsView
)
val
macs2
=
new
Macs2CallPeak
(
qscript
)
macs2
.
treatment
=
bamFile
macs2
.
treatment
=
bamFile
Filter
macs2
.
name
=
Some
(
sampleId
)
macs2
.
outputdir
=
sampleDir
+
File
.
separator
+
"macs2"
+
File
.
separator
+
sampleId
+
File
.
separator
add
(
macs2
)
...
...
@@ -155,8 +167,8 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
if
(!
samples
.
contains
(
controlId
))
throw
new
IllegalStateException
(
"For sample: "
+
sampleId
+
" this control: "
+
controlId
+
" does not exist"
)
val
macs2
=
new
Macs2CallPeak
(
this
)
macs2
.
treatment
=
sample
.
bamFile
macs2
.
control
=
samples
(
controlId
).
bamFile
macs2
.
treatment
=
sample
.
bamFile
Filter
macs2
.
control
=
samples
(
controlId
).
bamFile
Filter
macs2
.
name
=
Some
(
sampleId
+
"_VS_"
+
controlId
)
macs2
.
outputdir
=
sample
.
sampleDir
+
File
.
separator
+
"macs2"
+
File
.
separator
+
macs2
.
name
.
get
+
File
.
separator
add
(
macs2
)
...
...
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