Commit d11105a2 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Auto style changes

parent 094de5f1
......@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.utils
import java.io.File
import htsjdk.samtools._
import org.mockito.Mockito.{inOrder => inOrd}
import org.mockito.Mockito.{ inOrder => inOrd }
import org.scalatest.Matchers
import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.{BeforeClass, Test}
import org.testng.annotations.{ BeforeClass, Test }
/**
* Created by wyleung on 22-2-16.
......@@ -45,7 +45,6 @@ class BamUtilsTest extends TestNGSuite with MockitoSugar with Matchers {
new SAMLineParser(samh)
}
private val samHeaderTemplateErrornousNoReadgroup: SAMLineParser = {
val samh = new SAMFileHeader
samh.setSortOrder(SAMFileHeader.SortOrder.coordinate)
......@@ -178,29 +177,28 @@ class BamUtilsTest extends TestNGSuite with MockitoSugar with Matchers {
val thrown = intercept[IllegalArgumentException] {
sampleBamMap(List(BamUtilsTest.singleEndBam01WithDoubleSamples))
}
thrown.getMessage should ===("Bam contains multiple sample IDs: "+BamUtilsTest.singleEndBam01WithDoubleSamples)
thrown.getMessage should ===("Bam contains multiple sample IDs: " + BamUtilsTest.singleEndBam01WithDoubleSamples)
}
@Test def testSampleBamNamesMultipleSamplesPE = {
val thrown = intercept[IllegalArgumentException] {
sampleBamMap(List(BamUtilsTest.pairedEndBam01WithDoubleSamples))
}
thrown.getMessage should ===("Bam contains multiple sample IDs: "+BamUtilsTest.pairedEndBam01WithDoubleSamples)
thrown.getMessage should ===("Bam contains multiple sample IDs: " + BamUtilsTest.pairedEndBam01WithDoubleSamples)
}
@Test def testSampleBamNamesNoRGSE = {
val thrown = intercept[IllegalArgumentException] {
sampleBamMap(List(BamUtilsTest.singleEndBam01NoRG))
}
thrown.getMessage should ===("Bam does not contain sample ID or have no readgroups defined: "+BamUtilsTest.singleEndBam01NoRG)
thrown.getMessage should ===("Bam does not contain sample ID or have no readgroups defined: " + BamUtilsTest.singleEndBam01NoRG)
}
@Test def testSampleBamNamesNoRGPE = {
val thrown = intercept[IllegalArgumentException] {
sampleBamMap(List(BamUtilsTest.pairedEndBam01NoRG))
}
thrown.getMessage should ===("Bam does not contain sample ID or have no readgroups defined: "+BamUtilsTest.pairedEndBam01NoRG)
thrown.getMessage should ===("Bam does not contain sample ID or have no readgroups defined: " + BamUtilsTest.pairedEndBam01NoRG)
}
@Test def testSampleFoundTwice = {
......@@ -219,7 +217,6 @@ object BamUtilsTest {
var pairedEndBam02: File = File.createTempFile("bamutils", "paired02.bam")
singleEndBam01.deleteOnExit()
var singleEndBam01WithDoubleSamples: File = File.createTempFile("bamutils", "single01ds.bam")
singleEndBam01WithDoubleSamples.deleteOnExit()
var pairedEndBam01WithDoubleSamples: File = File.createTempFile("bamutils", "paired01ds.bam")
......@@ -229,6 +226,4 @@ object BamUtilsTest {
singleEndBam01NoRG.deleteOnExit()
var pairedEndBam01NoRG: File = File.createTempFile("bamutils", "paired01norg.bam")
singleEndBam01NoRG.deleteOnExit()
}
\ No newline at end of file
}
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