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biopet.biopet
Commits
9f3e8d4d
Commit
9f3e8d4d
authored
Apr 26, 2016
by
Peter van 't Hof
Browse files
Added objects again
parent
298ca175
Changes
12
Hide whitespace changes
Inline
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
View file @
9f3e8d4d
...
...
@@ -5,23 +5,6 @@
*/
package
nl.lumc.sasc.biopet.extensions.gatk.broad
//import java.io.File
//
//import nl.lumc.sasc.biopet.utils.config.Configurable
//
//class AnalyzeCovariates(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.AnalyzeCovariates with GatkGeneral {
//}
//
//object AnalyzeCovariates {
// def apply(root: Configurable, before: File, after: File, plots: File): AnalyzeCovariates = {
// val ac = new AnalyzeCovariates(root)
// ac.before = before
// ac.after = after
// ac.plots = plots
// ac
// }
//}
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
@@ -175,3 +158,13 @@ class AnalyzeCovariates(val root: Configurable) extends CommandLineGATK with Sca
conditional
(
filter_mismatching_base_and_quals
,
"-filterMBQ"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_bases_not_stored
,
"-filterNoBases"
,
escape
=
true
,
format
=
"%s"
)
}
object
AnalyzeCovariates
{
def
apply
(
root
:
Configurable
,
before
:
File
,
after
:
File
,
plots
:
File
)
:
AnalyzeCovariates
=
{
val
ac
=
new
AnalyzeCovariates
(
root
)
ac
.
before
=
before
ac
.
after
=
after
ac
.
plots
=
plots
ac
}
}
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
View file @
9f3e8d4d
...
...
@@ -15,14 +15,6 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
// if (config.contains("known_sites")) knownSites :+= new File(config("known_sites").asString)
//}
//
//object BaseRecalibrator {
// def apply(root: Configurable, input: File, output: File): BaseRecalibrator = {
// val br = new BaseRecalibrator(root)
// br.input_file :+= input
// br.out = output
// br
// }
//}
import
java.io.File
...
...
@@ -489,3 +481,12 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with S
conditional
(
filter_mismatching_base_and_quals
,
"-filterMBQ"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_bases_not_stored
,
"-filterNoBases"
,
escape
=
true
,
format
=
"%s"
)
}
object
BaseRecalibrator
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
)
:
BaseRecalibrator
=
{
val
br
=
new
BaseRecalibrator
(
root
)
br
.
input_file
:+=
input
br
.
out
=
output
br
}
}
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
View file @
9f3e8d4d
...
...
@@ -34,16 +34,6 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
// if (out.getName.endsWith(".vcf.gz")) vcfIndex = new File(out.getAbsolutePath + ".tbi")
// }
//}
//
//object GenotypeGVCFs {
// def apply(root: Configurable, gvcfFiles: List[File], output: File): GenotypeGVCFs = {
// val gg = new GenotypeGVCFs(root)
// gg.variant = gvcfFiles
// gg.out = output
// if (gg.out.getName.endsWith(".vcf.gz")) gg.vcfIndex = new File(gg.out.getAbsolutePath + ".tbi")
// gg
// }
//}
import
java.io.File
...
...
@@ -394,3 +384,13 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
conditional
(
filter_mismatching_base_and_quals
,
"-filterMBQ"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_bases_not_stored
,
"-filterNoBases"
,
escape
=
true
,
format
=
"%s"
)
}
object
GenotypeGVCFs
{
def
apply
(
root
:
Configurable
,
gvcfFiles
:
List
[
File
],
output
:
File
)
:
GenotypeGVCFs
=
{
val
gg
=
new
GenotypeGVCFs
(
root
)
gg
.
variant
=
gvcfFiles
gg
.
out
=
output
//if (gg.out.getName.endsWith(".vcf.gz")) gg.vcfIndex = new File(gg.out.getAbsolutePath + ".tbi")
gg
}
}
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
View file @
9f3e8d4d
...
...
@@ -57,23 +57,6 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
// }
//}
//
//object HaplotypeCaller {
// def apply(root: Configurable, inputFiles: List[File], outputFile: File): HaplotypeCaller = {
// val hc = new HaplotypeCaller(root)
// hc.input_file = inputFiles
// hc.out = outputFile
// if (hc.out.getName.endsWith(".vcf.gz")) hc.vcfIndex = new File(hc.out.getAbsolutePath + ".tbi")
// hc
// }
//
// def gvcf(root: Configurable, inputFile: File, outputFile: File): HaplotypeCaller = {
// val hc = apply(root, List(inputFile), outputFile)
// hc.emitRefConfidence = org.broadinstitute.gatk.tools.walkers.haplotypecaller.ReferenceConfidenceMode.GVCF
// hc.variant_index_type = GATKVCFIndexType.LINEAR
// hc.variant_index_parameter = Some(hc.config("variant_index_parameter", default = 128000).asInt)
// hc
// }
//}
import
java.io.File
...
...
@@ -81,6 +64,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk._
import
nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Input
,
_
}
import
org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
class
HaplotypeCaller
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
analysisName
=
"HaplotypeCaller"
...
...
@@ -1131,3 +1115,21 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
conditional
(
filter_mismatching_base_and_quals
,
"-filterMBQ"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_bases_not_stored
,
"-filterNoBases"
,
escape
=
true
,
format
=
"%s"
)
}
object
HaplotypeCaller
{
def
apply
(
root
:
Configurable
,
inputFiles
:
List
[
File
],
outputFile
:
File
)
:
HaplotypeCaller
=
{
val
hc
=
new
HaplotypeCaller
(
root
)
hc
.
input_file
=
inputFiles
hc
.
out
=
outputFile
//if (hc.out.getName.endsWith(".vcf.gz")) hc.vcfIndex = new File(hc.out.getAbsolutePath + ".tbi")
hc
}
def
gvcf
(
root
:
Configurable
,
inputFile
:
File
,
outputFile
:
File
)
:
HaplotypeCaller
=
{
val
hc
=
apply
(
root
,
List
(
inputFile
),
outputFile
)
hc
.
emitRefConfidence
=
"GVCF"
hc
.
variant_index_type
=
GATKVCFIndexType
.
LINEAR
hc
.
variant_index_parameter
=
Some
(
hc
.
config
(
"variant_index_parameter"
,
default
=
128000
).
asInt
)
hc
}
}
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
View file @
9f3e8d4d
...
...
@@ -5,31 +5,6 @@
*/
package
nl.lumc.sasc.biopet.extensions.gatk.broad
//import java.io.File
//
//import nl.lumc.sasc.biopet.utils.config.Configurable
//import org.broadinstitute.gatk.utils.commandline.{ Gather, Output }
//
//class IndelRealigner(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.IndelRealigner with GatkGeneral {
//
// @Gather(enabled = false)
// @Output
// protected var bamIndex: File = _
//
// if (config.contains("scattercount")) scatterCount = config("scattercount")
//}
//
//object IndelRealigner {
// def apply(root: Configurable, input: File, targetIntervals: File, outputDir: File): IndelRealigner = {
// val ir = new IndelRealigner(root)
// ir.input_file :+= input
// ir.targetIntervals = targetIntervals
// ir.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bam")
// ir.bamIndex = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.bai")
// ir
// }
//}
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
@@ -430,3 +405,14 @@ class IndelRealigner(val root: Configurable) extends CommandLineGATK with Scatte
conditional
(
filter_mismatching_base_and_quals
,
"-filterMBQ"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_bases_not_stored
,
"-filterNoBases"
,
escape
=
true
,
format
=
"%s"
)
}
object
IndelRealigner
{
def
apply
(
root
:
Configurable
,
input
:
File
,
targetIntervals
:
File
,
outputDir
:
File
)
:
IndelRealigner
=
{
val
ir
=
new
IndelRealigner
(
root
)
ir
.
input_file
:+=
input
ir
.
targetIntervals
=
targetIntervals
ir
.
out
=
new
File
(
outputDir
,
input
.
getName
.
stripSuffix
(
".bam"
)
+
".realign.bam"
)
ir
.
deps
:+=
new
File
(
outputDir
,
input
.
getName
.
stripSuffix
(
".bam"
)
+
".realign.bai"
)
ir
}
}
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala
View file @
9f3e8d4d
...
...
@@ -5,23 +5,6 @@
*/
package
nl.lumc.sasc.biopet.extensions.gatk.broad
//import java.io.File
//
//import nl.lumc.sasc.biopet.utils.config.Configurable
//
//class PrintReads(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.PrintReads with GatkGeneral {
// if (config.contains("scattercount")) scatterCount = config("scattercount")
//}
//
//object PrintReads {
// def apply(root: Configurable, input: File, output: File): PrintReads = {
// val br = new PrintReads(root)
// br.input_file :+= input
// br.out = output
// br
// }
//}
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
@@ -221,3 +204,12 @@ class PrintReads(val root: Configurable) extends CommandLineGATK with ScatterGat
conditional
(
filter_mismatching_base_and_quals
,
"-filterMBQ"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_bases_not_stored
,
"-filterNoBases"
,
escape
=
true
,
format
=
"%s"
)
}
object
PrintReads
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
)
:
PrintReads
=
{
val
br
=
new
PrintReads
(
root
)
br
.
input_file
:+=
input
br
.
out
=
output
br
}
}
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala
View file @
9f3e8d4d
...
...
@@ -5,25 +5,6 @@
*/
package
nl.lumc.sasc.biopet.extensions.gatk.broad
//import java.io.File
//
//import nl.lumc.sasc.biopet.utils.config.Configurable
//
//class RealignerTargetCreator(val root: Configurable) extends org.broadinstitute.gatk.queue.extensions.gatk.RealignerTargetCreator with GatkGeneral {
// if (config.contains("scattercount")) scatterCount = config("scattercount")
//
// if (config.contains("known")) known ++= config("known").asFileList
//}
//
//object RealignerTargetCreator {
// def apply(root: Configurable, input: File, outputDir: File): RealignerTargetCreator = {
// val re = new RealignerTargetCreator(root)
// re.input_file :+= input
// re.out = new File(outputDir, input.getName.stripSuffix(".bam") + ".realign.intervals")
// re
// }
//}
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
@@ -194,3 +175,12 @@ class RealignerTargetCreator(val root: Configurable) extends CommandLineGATK wit
conditional
(
filter_mismatching_base_and_quals
,
"-filterMBQ"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_bases_not_stored
,
"-filterNoBases"
,
escape
=
true
,
format
=
"%s"
)
}
object
RealignerTargetCreator
{
def
apply
(
root
:
Configurable
,
input
:
File
,
outputDir
:
File
)
:
RealignerTargetCreator
=
{
val
re
=
new
RealignerTargetCreator
(
root
)
re
.
input_file
:+=
input
re
.
out
=
new
File
(
outputDir
,
input
.
getName
.
stripSuffix
(
".bam"
)
+
".realign.intervals"
)
re
}
}
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
View file @
9f3e8d4d
...
...
@@ -44,17 +44,6 @@ package nl.lumc.sasc.biopet.extensions.gatk.broad
// memoryLimit = Option(nct.getOrElse(1) * memoryLimit.getOrElse(2.0))
// }
//}
//
//object UnifiedGenotyper {
// def apply(root: Configurable, inputFiles: List[File], outputFile: File): UnifiedGenotyper = {
// val ug = new UnifiedGenotyper(root)
// ug.input_file = inputFiles
// ug.out = outputFile
// if (ug.out.getName.endsWith(".vcf.gz")) ug.vcfIndex = new File(ug.out.getAbsolutePath + ".tbi")
// ug
// }
//
//}
import
java.io.File
...
...
@@ -892,3 +881,13 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
conditional
(
filter_mismatching_base_and_quals
,
"-filterMBQ"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_bases_not_stored
,
"-filterNoBases"
,
escape
=
true
,
format
=
"%s"
)
}
object
UnifiedGenotyper
{
def
apply
(
root
:
Configurable
,
inputFiles
:
List
[
File
],
outputFile
:
File
)
:
UnifiedGenotyper
=
{
val
ug
=
new
UnifiedGenotyper
(
root
)
ug
.
input_file
=
inputFiles
ug
.
out
=
outputFile
//if (ug.out.getName.endsWith(".vcf.gz")) ug.vcfIndex = new File(ug.out.getAbsolutePath + ".tbi")
ug
}
}
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
View file @
9f3e8d4d
...
...
@@ -28,8 +28,8 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
CatVariantsGatherer
,
GATKScatterFunction
,
LocusScatterFunction
,
TaggedFile
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Output
,
_
}
import
org.broadinstitute.gatk.queue.extensions.gatk.
{
CatVariantsGatherer
,
GATKScatterFunction
,
LocusScatterFunction
,
TaggedFile
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Output
,
_
}
class
VariantAnnotator
(
val
root
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
analysisName
=
"VariantAnnotator"
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/HaplotypeCallerAllele.scala
View file @
9f3e8d4d
...
...
@@ -17,7 +17,7 @@ class HaplotypeCallerAllele(val root: Configurable) extends Variantcaller {
def
biopetScript
()
{
val
hc
=
broad
.
HaplotypeCaller
(
this
,
inputBams
.
values
.
toList
,
outputFile
)
hc
.
alleles
=
config
(
"input_alleles"
)
hc
.
genotyping_mode
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
genotyper
.
GenotypingOutputMode
.
GENOTYPE_GIVEN_ALLELES
hc
.
genotyping_mode
=
"
GENOTYPE_GIVEN_ALLELES
"
add
(
hc
)
}
}
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyperAllele.scala
View file @
9f3e8d4d
...
...
@@ -17,7 +17,7 @@ class UnifiedGenotyperAllele(val root: Configurable) extends Variantcaller {
def
biopetScript
()
{
val
ug
=
broad
.
UnifiedGenotyper
(
this
,
inputBams
.
values
.
toList
,
outputFile
)
ug
.
alleles
=
config
(
"input_alleles"
)
ug
.
genotyping_mode
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
genotyper
.
GenotypingOutputMode
.
GENOTYPE_GIVEN_ALLELES
ug
.
genotyping_mode
=
"
GENOTYPE_GIVEN_ALLELES
"
add
(
ug
)
}
}
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ScatterGatherableFunction.scala
View file @
9f3e8d4d
package
nl.lumc.sasc.biopet.core
/**
* Created by pjvan_thof on 4/26/16.
*/
* Created by pjvan_thof on 4/26/16.
*/
trait
ScatterGatherableFunction
extends
BiopetCommandLineFunction
with
org
.
broadinstitute
.
gatk
.
queue
.
function
.
scattergather
.
ScatterGatherableFunction
{
scatterCount
=
config
(
"scatter_count"
,
freeVar
=
true
)
...
...
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