Commit f6bfca5d authored by Peter van 't Hof's avatar Peter van 't Hof

Switch to Queue 3.6

parent e5d79321
......@@ -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>
......
......@@ -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 {
......
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