Commit 6744e672 authored by bow's avatar bow
Browse files

Merge branch 'feature-queue_3.6' into 'develop'

Switch to Queue 3.6

Fixes #335 and biopet/Biopet-FunctionalTests#25

See merge request !420
parents e5d79321 f841b758
......@@ -56,7 +56,7 @@
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-queue</artifactId>
<version>3.5</version>
<version>3.6</version>
<exclusions>
<exclusion>
<groupId>org.broadinstitute.gatk</groupId>
......@@ -67,7 +67,7 @@
<dependency>
<groupId>org.broadinstitute.gatk</groupId>
<artifactId>gatk-queue-extensions-public</artifactId>
<version>3.5</version>
<version>3.6</version>
</dependency>
<dependency>
<groupId>org.scalatra.scalate</groupId>
......
......@@ -16,17 +16,16 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import nl.lumc.sasc.biopet.utils.VcfUtils
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, _ }
import org.broadinstitute.gatk.utils.commandline.{ Argument, Gather, Output, Input }
//TODO: check gathering
class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with ScatterGatherableFunction */ {
class BaseRecalibrator(val root: Configurable) extends CommandLineGATK with ScatterGatherableFunction {
def analysis_type = "BaseRecalibrator"
//TODO: check gathering
//scatterClass = classOf[ContigScatterFunction]
//setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
scatterClass = classOf[ContigScatterFunction]
setupScatterFunction = { case scatter: GATKScatterFunction => scatter.includeUnmapped = false }
/** A database of known polymorphic sites */
@Input(fullName = "knownSites", shortName = "knownSites", doc = "A database of known polymorphic sites", required = false, exclusiveOf = "", validation = "")
......@@ -38,7 +37,7 @@ class BaseRecalibrator(val root: Configurable) extends CommandLineGATK /* with S
/** The output recalibration table file to create */
@Output(fullName = "out", shortName = "o", doc = "The output recalibration table file to create", required = true, exclusiveOf = "", validation = "") //TODO: check gathering
//@Gather(classOf[org.broadinstitute.gatk.engine.recalibration.BQSRGatherer])
@Gather(classOf[org.broadinstitute.gatk.engine.recalibration.BQSRGatherer])
var out: File = _
/** One or more covariates to be used in the recalibration. Can be specified multiple times */
......
......@@ -65,7 +65,7 @@
<dependency>
<groupId>com.github.broadinstitute</groupId>
<artifactId>picard</artifactId>
<version>1.141</version>
<version>2.4.1</version>
</dependency>
</dependencies>
</project>
\ No newline at end of file
......@@ -177,10 +177,10 @@ object VcfWithVcf extends ToolCommand {
def getSecondaryRecords(secondaryReader: VCFFileReader,
record: VariantContext, matchAllele: Boolean): List[VariantContext] = {
if (matchAllele) {
secondaryReader.query(record.getContig, record.getStart, record.getEnd).toList.
filter(x => record.getAlternateAlleles.exists(x.hasAlternateAllele))
secondaryReader.query(record.getContig, record.getStart, record.getEnd).
filter(x => record.getAlternateAlleles.exists(x.hasAlternateAllele)).toList
} else {
secondaryReader.query(record.getContig, record.getStart, record.getEnd).toList
secondaryReader.query(record.getContig, record.getStart, record.getEnd).toIterable.toList
}
}
......
......@@ -66,7 +66,7 @@
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
<version>1.141</version>
<version>2.4.1</version>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
......
......@@ -11,8 +11,8 @@ import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
/**
* Created by pjvan_thof on 31-5-16.
*/
* Created by pjvan_thof on 31-5-16.
*/
class Impute2VcfTest extends TestNGSuite with Matchers {
def initPipeline(map: Map[String, Any]): Impute2Vcf = {
new Impute2Vcf {
......
......@@ -28,7 +28,7 @@ class HaplotypeCallerAllele(val root: Configurable) extends Variantcaller {
val name = "haplotypecaller_allele"
protected def defaultPrio = 5
val alleles: File = config("input_alleles")
lazy val alleles: File = config("input_alleles")
def biopetScript() {
val hc = gatk.HaplotypeCaller(this, inputBams.values.toList, outputFile)
......
......@@ -27,7 +27,7 @@ class UnifiedGenotyperAllele(val root: Configurable) extends Variantcaller {
val name = "unifiedgenotyper_allele"
protected def defaultPrio = 9
val alleles: File = config("input_alleles")
lazy val alleles: File = config("input_alleles")
def biopetScript() {
val ug = gatk.UnifiedGenotyper(this, inputBams.values.toList, outputFile)
......
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