Commit 0d010c88 authored by Sander van der Zeeuw's avatar Sander van der Zeeuw
Browse files

changed imports

parent 025740f5
...@@ -18,12 +18,12 @@ package nl.lumc.sasc.biopet.pipelines.shiva ...@@ -18,12 +18,12 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.summary.SummaryQScript import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{Reference, SampleLibraryTag} import nl.lumc.sasc.biopet.core.{ Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.bcftools.{BcftoolsCall, BcftoolsMerge} import nl.lumc.sasc.biopet.extensions.bcftools.{ BcftoolsCall, BcftoolsMerge }
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import nl.lumc.sasc.biopet.extensions.tools.{MpileupToVcf, VcfFilter, VcfStats} import nl.lumc.sasc.biopet.extensions.tools.{ MpileupToVcf, VcfFilter, VcfStats }
import nl.lumc.sasc.biopet.extensions.{Bgzip, Tabix} import nl.lumc.sasc.biopet.extensions.{ Bgzip, Tabix }
import nl.lumc.sasc.biopet.utils.Logging import nl.lumc.sasc.biopet.utils.Logging
import org.broadinstitute.gatk.utils.commandline.Input import org.broadinstitute.gatk.utils.commandline.Input
......
...@@ -49,11 +49,13 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers { ...@@ -49,11 +49,13 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
@DataProvider(name = "shivaVariantcallingOptions") @DataProvider(name = "shivaVariantcallingOptions")
def shivaVariantcallingOptions = { def shivaVariantcallingOptions = {
val bool = Array(true, false) val bool = Array(true, false)
(for (bams <- 0 to 3; (for (
raw <- bool; bams <- 0 to 3;
bcftools <- bool; raw <- bool;
bcftools_singlesample <- bool; bcftools <- bool;
freebayes <- bool) yield Array(bams, raw, bcftools, bcftools_singlesample, freebayes)).toArray bcftools_singlesample <- bool;
freebayes <- bool
) yield Array(bams, raw, bcftools, bcftools_singlesample, freebayes)).toArray
} }
@Test(dataProvider = "shivaVariantcallingOptions") @Test(dataProvider = "shivaVariantcallingOptions")
...@@ -72,7 +74,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers { ...@@ -72,7 +74,7 @@ class ShivaVariantcallingTest extends TestNGSuite with Matchers {
pipeline.inputBams = (for (n <- 1 to bams) yield ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toList pipeline.inputBams = (for (n <- 1 to bams) yield ShivaVariantcallingTest.inputTouch("bam_" + n + ".bam")).toList
val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !freebayes) val illegalArgumentException = pipeline.inputBams.isEmpty || (!raw && !bcftools && !bcftools_singlesample && !freebayes)
if (illegalArgumentException) intercept[IllegalArgumentException] { if (illegalArgumentException) intercept[IllegalArgumentException] {
pipeline.script() pipeline.script()
......
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