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biopet.biopet
Commits
1c334578
Commit
1c334578
authored
Apr 27, 2016
by
Peter van 't Hof
Browse files
Fix compile errors
parent
412df3fe
Changes
8
Hide whitespace changes
Inline
Side-by-side
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
1c334578
...
...
@@ -98,7 +98,7 @@ object BammetricsReport extends ReportBuilder {
/**
* Generate a stackbar plot for alignment stats
*
*
* @param outputDir OutputDir for the tsv and png file
* @param prefix Prefix of the tsv and png file
* @param summary Summary class
...
...
@@ -162,7 +162,7 @@ object BammetricsReport extends ReportBuilder {
/**
* Generate a line plot for insertsize
*
*
* @param outputDir OutputDir for the tsv and png file
* @param prefix Prefix of the tsv and png file
* @param summary Summary class
...
...
@@ -251,7 +251,7 @@ object BammetricsReport extends ReportBuilder {
/**
* Generate a line plot for wgs coverage
*
*
* @param outputDir OutputDir for the tsv and png file
* @param prefix Prefix of the tsv and png file
* @param summary Summary class
...
...
@@ -342,7 +342,7 @@ object BammetricsReport extends ReportBuilder {
/**
* Generate a line plot for rna coverage
*
*
* @param outputDir OutputDir for the tsv and png file
* @param prefix Prefix of the tsv and png file
* @param summary Summary class
...
...
basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
1c334578
...
...
@@ -24,7 +24,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.
{
MultiSampleQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions.
{
Cat
,
Raxml
,
RunGubbins
}
import
nl.lumc.sasc.biopet.pipelines.shiva.
{
Shiva
,
ShivaTrait
}
import
nl.lumc.sasc.biopet.pipelines.shiva.Shiva
import
nl.lumc.sasc.biopet.extensions.tools.BastyGenerateFasta
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
@@ -44,7 +44,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
"variantcallers"
->
variantcallers
)
lazy
val
shiva
:
ShivaTrait
=
new
Shiva
(
qscript
)
lazy
val
shiva
=
new
Shiva
(
qscript
)
def
summaryFile
:
File
=
new
File
(
outputDir
,
"Basty.summary.json"
)
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
1c334578
...
...
@@ -205,11 +205,12 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
logger
.
info
(
s
"Starting script for ${samples.size} samples"
)
var
count
=
0
if
(
onlySamples
.
isEmpty
||
samples
.
forall
(
x
=>
onlySamples
.
contains
(
x
.
_1
)))
{
samples
.
foreach
{
case
(
sampleId
,
sample
)
=>
logger
.
info
(
s
"Starting script sample '$sampleId'"
)
sample
.
addAndTrackJobs
()
count
+=
1
logger
.
info
(
s
"Finish script for '$sampleId', samples done: $count / ${samples.size}"
)
samples
.
foreach
{
case
(
sampleId
,
sample
)
=>
logger
.
info
(
s
"Starting script sample '$sampleId'"
)
sample
.
addAndTrackJobs
()
count
+=
1
logger
.
info
(
s
"Finish script for '$sampleId', samples done: $count / ${samples.size}"
)
}
logger
.
info
(
"Starting script for multisample jobs"
)
addMultiSampleJobs
()
...
...
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @
1c334578
...
...
@@ -189,7 +189,7 @@ trait ReportBuilder extends ToolCommand {
/**
* This method will render the page and the subpages recursivly
*
*
* @param summary The summary object
* @param page Page to render
* @param outputDir Root output dir of the report
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
1c334578
...
...
@@ -120,7 +120,7 @@ object ShivaReport extends MultisampleMappingReportTrait {
/**
* Generate a stackbar plot for found variants
*
*
* @param outputDir OutputDir for the tsv and png file
* @param prefix Prefix of the tsv and png file
* @param summary Summary class
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
View file @
1c334578
...
...
@@ -22,7 +22,6 @@ import nl.lumc.sasc.biopet.extensions.gatk.{ CombineVariants, GenotypeConcordanc
import
nl.lumc.sasc.biopet.extensions.tools.VcfStats
import
nl.lumc.sasc.biopet.extensions.vt.
{
VtDecompose
,
VtNormalize
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
import
nl.lumc.sasc.biopet.pipelines.gatk.variantcallers._
import
nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.
{
VarscanCnsSingleSample
,
_
}
import
nl.lumc.sasc.biopet.utils.
{
BamUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
View file @
1c334578
...
...
@@ -15,7 +15,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.extensions.gatk.broad._
...
...
@@ -26,13 +26,13 @@ import nl.lumc.sasc.biopet.utils.config.Config
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
DataProvider
,
Test
}
import
org.testng.annotations.
{
DataProvider
,
Test
}
/**
* Class for testing shiva
*
* Created by pjvan_thof on 3/2/15.
*/
* Class for testing shiva
*
* Created by pjvan_thof on 3/2/15.
*/
class
ShivaTest
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
Shiva
=
{
new
Shiva
()
{
...
...
shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
View file @
1c334578
/**
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
* Due to the license issue with GATK, this part of Biopet can only be used inside the
* LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
* on how to use this protected part of biopet or contact us at sasc@lumc.nl
*/
package
nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.
{
File
,
FileOutputStream
}
import
java.io.
{
File
,
FileOutputStream
}
import
com.google.common.io.Files
import
nl.lumc.sasc.biopet.core.BiopetPipe
import
nl.lumc.sasc.biopet.extensions.Freebayes
import
nl.lumc.sasc.biopet.extensions.bcftools.
{
BcftoolsCall
,
BcftoolsMerge
}
import
nl.lumc.sasc.biopet.extensions.bcftools.
{
BcftoolsCall
,
BcftoolsMerge
}
import
nl.lumc.sasc.biopet.utils.config.Config
import
nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
HaplotypeCaller
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.extensions.gatk.broad.
{
HaplotypeCaller
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcalling
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
org.apache.commons.io.FileUtils
import
org.broadinstitute.gatk.queue.QSettings
import
org.scalatest.Matchers
import
org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
import
org.testng.annotations.
{
AfterClass
,
DataProvider
,
Test
}
import
scala.collection.mutable.ListBuffer
/**
* Class for testing ShivaVariantcalling
*
* Created by pjvan_thof on 3/2/15.
*/
* Class for testing ShivaVariantcalling
*
* Created by pjvan_thof on 3/2/15.
*/
class
ShivaVariantcallingTest
extends
TestNGSuite
with
Matchers
{
def
initPipeline
(
map
:
Map
[
String
,
Any
])
:
ShivaVariantcalling
=
{
new
ShivaVariantcalling
()
{
...
...
@@ -55,7 +55,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
unifiedGenotyper
<-
bool
;
haplotypeCaller
<-
bool
)
yield
Array
[
Any
](
bams
,
raw
,
bcftools
,
bcftools_singlesample
,
unifiedGenotyper
,
haplotypeCaller
,
haplotypeCallerGvcf
,
haplotypeCallerAllele
,
unifiedGenotyperAllele
)
).
toArray
).
toArray
}
@Test
(
dataProvider
=
"shivaVariantcallingOptions"
)
...
...
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