Commit ec4eb7de authored by Peter van 't Hof's avatar Peter van 't Hof

Style fixes

parent 03360822
......@@ -3,13 +3,13 @@ package nl.lumc.sasc.biopet.pipelines.mapping
import java.io.{File, FileOutputStream}
import com.google.common.io.Files
import nl.lumc.sasc.biopet.extensions.picard.{MarkDuplicates, MergeSamFiles}
import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, MergeSamFiles }
import nl.lumc.sasc.biopet.utils.ConfigUtils
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 }
/**
* Created by pjvanthof on 15/05/16.
......@@ -27,6 +27,7 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
def mergeStrategies = MultisampleMapping.MergeStrategy.values
def bamToFastq = false
def correctReadgroups = false
def unmappedToGears = false
def sample1 = Array(true, false)
def sample2 = Array(true, false)
......@@ -43,7 +44,12 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
var m: Map[String, Any] = MultisampleMappingTestTrait.config
if (sample1) m = ConfigUtils.mergeMaps(MultisampleMappingTestTrait.sample1, m)
if (sample2) m = ConfigUtils.mergeMaps(MultisampleMappingTestTrait.sample2, m)
m ++ Map("merge_strategy" -> merge.toString, "bam_to_fastq" -> bamToFastq, "correct_readgroups" -> correctReadgroups)
m ++ Map(
"merge_strategy" -> merge.toString,
"bam_to_fastq" -> bamToFastq,
"correct_readgroups" -> correctReadgroups,
"unmapped_to_gears" -> unmappedToGears
)
}
if (!sample1 && !sample2) { // When no samples
......@@ -64,7 +70,12 @@ trait MultisampleMappingTestTrait extends TestNGSuite with Matchers {
(if (sample2 && (merge == MergeStrategy.MergeSam || merge == MergeStrategy.PreProcessMergeSam)) 1 else 0))
pipeline.samples.foreach { case (sampleName, sample) =>
if (merge == MergeStrategy.None) sample.bamFile shouldBe None
sample.summaryStats shouldBe Map()
sample.libraries.foreach { case (libraryId, library) =>
library.summaryStats shouldBe Map()
}
}
pipeline.summarySettings.get("merge_strategy") shouldBe Some(merge.toString)
}
}
}
......
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