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biopet.biopet
Commits
836310ca
Commit
836310ca
authored
Jun 23, 2015
by
Peter van 't Hof
Browse files
Fix reference
parent
40f1af70
Changes
4
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
View file @
836310ca
...
...
@@ -17,20 +17,20 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.
{
Reference
,
BiopetCommandLineFunction
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Created by pjvan_thof on 3/3/15.
*/
class
Freebayes
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
class
Freebayes
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
{
@Input
(
required
=
true
)
var
bamfiles
:
List
[
File
]
=
Nil
@Input
(
required
=
true
)
var
reference
:
File
=
config
(
"reference"
)
var
reference
:
File
=
_
@Output
(
required
=
true
)
var
outputVcf
:
File
=
null
...
...
@@ -42,6 +42,11 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction {
override
val
versionRegex
=
"""version: (.*)"""
.
r
override
def
versionCommand
=
executable
+
" --version"
override
def
beforeGraph
:
Unit
=
{
super
.
beforeGraph
reference
=
referenceFasta
()
}
def
cmdLine
=
executable
+
required
(
"--fasta-reference"
,
reference
)
+
repeat
(
"--bam"
,
bamfiles
)
+
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsMpileup.scala
View file @
836310ca
...
...
@@ -15,12 +15,13 @@
*/
package
nl.lumc.sasc.biopet.extensions.samtools
import
nl.lumc.sasc.biopet.core.Reference
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
java.io.File
/** Extension for samtools mpileup */
class
SamtoolsMpileup
(
val
root
:
Configurable
)
extends
Samtools
{
class
SamtoolsMpileup
(
val
root
:
Configurable
)
extends
Samtools
with
Reference
{
@Input
(
doc
=
"Bam File"
)
var
input
:
List
[
File
]
=
Nil
...
...
@@ -28,7 +29,7 @@ class SamtoolsMpileup(val root: Configurable) extends Samtools {
var
output
:
File
=
_
@Input
(
doc
=
"Reference fasta"
)
var
reference
:
File
=
config
(
"reference"
)
var
reference
:
File
=
_
@Input
(
doc
=
"Interval bed"
,
required
=
false
)
var
intervalBed
:
Option
[
File
]
=
config
(
"interval_bed"
)
...
...
@@ -40,6 +41,11 @@ class SamtoolsMpileup(val root: Configurable) extends Samtools {
var
depth
:
Option
[
Int
]
=
config
(
"depth"
)
var
outputMappingQuality
:
Boolean
=
config
(
"output_mapping_quality"
,
default
=
false
)
override
def
beforeGraph
:
Unit
=
{
super
.
beforeGraph
reference
=
referenceFasta
()
}
def
cmdBase
=
required
(
executable
)
+
required
(
"mpileup"
)
+
optional
(
"-f"
,
reference
)
+
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
View file @
836310ca
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.tools
import
java.io.File
import
java.io.PrintWriter
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import
nl.lumc.sasc.biopet.utils.ConfigUtils
...
...
@@ -29,7 +29,7 @@ import scala.math.round
import
scala.math.floor
import
scala.collection.JavaConversions._
class
MpileupToVcf
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
class
MpileupToVcf
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
with
Reference
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input mpileup file"
,
shortName
=
"mpileup"
,
required
=
false
)
...
...
@@ -46,7 +46,7 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion {
var
homoFraction
:
Option
[
Double
]
=
config
(
"homoFraction"
)
var
ploidy
:
Option
[
Int
]
=
config
(
"ploidy"
)
var
sample
:
String
=
_
var
reference
:
String
=
config
(
"reference"
)
var
reference
:
String
=
_
override
val
defaultCoreMemory
=
3.0
...
...
@@ -55,6 +55,7 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion {
override
def
beforeGraph
{
super
.
beforeGraph
reference
=
referenceFasta
().
getAbsolutePath
val
samtoolsMpileup
=
new
SamtoolsMpileup
(
this
)
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
View file @
836310ca
...
...
@@ -21,7 +21,7 @@ import htsjdk.samtools.reference.FastaSequenceFile
import
htsjdk.variant.variantcontext.
{
Allele
,
VariantContext
,
Genotype
}
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.core.summary.
{
SummaryQScript
,
Summarizable
}
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
import
scala.collection.JavaConversions._
...
...
@@ -35,7 +35,7 @@ import scala.util.Random
/**
* Created by pjvan_thof on 1/10/15.
*/
class
VcfStats
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
with
Summarizable
{
class
VcfStats
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
with
Summarizable
with
Reference
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input fastq"
,
shortName
=
"I"
,
required
=
true
)
...
...
@@ -59,9 +59,10 @@ class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summariza
var
genotypeTags
:
List
[
String
]
=
Nil
var
allInfoTags
=
false
var
allGenotypeTags
=
false
var
reference
:
File
=
config
(
"reference"
)
var
reference
:
File
=
_
override
def
beforeGraph
:
Unit
=
{
reference
=
referenceFasta
()
index
=
new
File
(
input
.
getAbsolutePath
+
".tbi"
)
}
...
...
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