diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
index 233e7c4fdbd662be3387ebef2a78ef292c0a7487..98bf67973dcee391d2c19d29a39d52ff34f8675f 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
@@ -24,7 +24,7 @@ import org.testng.annotations.{ DataProvider, Test }
* Created by pjvan_thof on 1/8/15.
*/
class ConfigTest extends TestNGSuite with Matchers with ConfigUtils.ImplicitConversions {
- @Test def testLoadConfigFile: Unit = {
+ @Test def testLoadConfigFile(): Unit = {
val config = new Config
config.loadConfigFile(ConfigTest.file)
config.map shouldBe ConfigTest.map
@@ -32,7 +32,7 @@ class ConfigTest extends TestNGSuite with Matchers with ConfigUtils.ImplicitConv
config.map shouldBe ConfigTest.map
}
- @Test def testContains: Unit = {
+ @Test def testContains(): Unit = {
ConfigTest.config.contains("m1") shouldBe true
ConfigTest.config.contains("notexist") shouldBe false
ConfigTest.config.contains(new ConfigValueIndex("m1", Nil, "k1")) shouldBe true
@@ -40,23 +40,23 @@ class ConfigTest extends TestNGSuite with Matchers with ConfigUtils.ImplicitConv
ConfigTest.config.contains(new ConfigValueIndex("notexist", Nil, "k1", false)) shouldBe false
}
- @Test def testApply: Unit = {
+ @Test def testApply(): Unit = {
ConfigTest.config("m1", Nil, "k1").asString shouldBe "v2"
ConfigTest.config("m1", Nil, "notexist", default = "default").asString shouldBe "default"
}
- @Test def testMergeConfigs: Unit = {
+ @Test def testMergeConfigs(): Unit = {
val map1 = Map("1" -> 1)
val map2 = Map("2" -> 2)
Config.mergeConfigs(new Config(map1), new Config(map2)).map shouldBe ConfigUtils.mergeMaps(map1, map2)
}
- @Test def testToString: Unit = {
+ @Test def testToString(): Unit = {
val map1 = Map("1" -> 1)
new Config(map1).toString() shouldBe map1.toString()
}
- @Test def testSkipNested: Unit = {
+ @Test def testSkipNested(): Unit = {
val map = Map("1" -> Map("2" -> Map("4" -> Map("5" -> Map("k1" -> "v1")))))
Config.getValueFromMap(map, new ConfigValueIndex("5", List("1", "2", "4", "5"), "k1")).get.asString shouldBe "v1"
Config.getValueFromMap(map, new ConfigValueIndex("5", List("1", "2", "3", "4", "5"), "k1")).get.asString shouldBe "v1"
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigValueTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigValueTest.scala
index 9fdfec9923c1fecbba1d6051b7693ac560f456ce..190ca1bd9d18a5e4ecd1232dca8526a05fa829b0 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigValueTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigValueTest.scala
@@ -26,7 +26,7 @@ import org.testng.annotations.Test
*/
class ConfigValueTest extends TestNGSuite with Matchers {
val index = ConfigValueIndex("", Nil, "")
- @Test def testAs: Unit = {
+ @Test def testAs(): Unit = {
ConfigValue(index, index, "bla").asString shouldBe "bla"
ConfigValue(index, index, 1).asInt shouldBe 1
ConfigValue(index, index, 1.0).asDouble shouldBe 1.0
@@ -37,7 +37,7 @@ class ConfigValueTest extends TestNGSuite with Matchers {
ConfigValue(index, index, List("bla")).asFileList shouldBe List(new File("bla"))
}
- @Test def testToString: Unit = {
- ConfigValue(index, index, "bla", true).toString.getClass.getSimpleName shouldBe "String"
+ @Test def testToString(): Unit = {
+ ConfigValue(index, index, "bla", default = true).toString.getClass.getSimpleName shouldBe "String"
}
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
index 7390dc7ca9bcc5c2896438c21fa2ce80e1757b59..941f2ca9d45b96e6c756ff1ce70d9644642fdc09 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
@@ -23,7 +23,7 @@ import org.testng.annotations.Test
* Created by pjvan_thof on 1/8/15.
*/
class ConfigurableTest extends TestNGSuite with Matchers {
- @Test def testConfigurable: Unit = {
+ @Test def testConfigurable(): Unit = {
val classC = new ClassC {
override def configName = "classc"
override val globalConfig = new Config(ConfigurableTest.map)
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
index d775d8c59459879c9465169d22be891fc2b96617..1ffd257e0a53c23ce37812601e8b63464cc2dd37 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/GsnapTest.scala
@@ -26,7 +26,7 @@ import scala.sys.process.{ Process, ProcessLogger }
class GsnapTest extends TestNGSuite with Matchers {
private def setConfig(key: String, value: String): Map[String, Any] = {
- val oldMap: Map[String, Any] = Config.global.map.toMap
+ val oldMap: Map[String, Any] = Config.global.map
Config.global.map += (key -> value)
oldMap
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
index 4a2cd7aa149bf665f2b91f42b29bef9ab52d9d0b..a4de59d895a43fd4110f4745d1011b2bad4c23d5 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
@@ -28,7 +28,7 @@ import org.testng.annotations.Test
class CollectAlignmentSummaryMetricsTest extends TestNGSuite with Matchers {
@Test
- def summaryData: Unit = {
+ def summaryData(): Unit = {
val file = new File(Paths.get(getClass.getResource("/picard.alignmentMetrics").toURI).toString)
val job = new CollectAlignmentSummaryMetrics(null)
job.output = file
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
index 09dabd796130930912af9909b644843d61c51c94..8439019c482361289d98452cd7543be0499fee0f 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
@@ -28,7 +28,7 @@ import org.testng.annotations.Test
class CollectInsertSizeMetricsTest extends TestNGSuite with Matchers {
@Test
- def summaryData: Unit = {
+ def summaryData(): Unit = {
val file = new File(Paths.get(getClass.getResource("/picard.insertsizemetrics").toURI).toString)
val job = new CollectInsertSizeMetrics(null)
job.output = file
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
index fe0d71a22f387f2586973410b19689e13525333b..57ba12abfad4dbfc2205c40e94873d1c29789936 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
@@ -28,7 +28,7 @@ import org.testng.annotations.Test
class MarkDuplicatesTest extends TestNGSuite with Matchers {
@Test
- def summaryData: Unit = {
+ def summaryData(): Unit = {
val file = new File(Paths.get(getClass.getResource("/picard.dedup.metrics").toURI).toString)
val job = new MarkDuplicates(null)
job.outputMetrics = file
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
index 07bd5ed162a1af2e840c067df997e6456145af74..565498eb6ed0732c1c796f4cf82d91d77a55815b 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/FastqSyncTest.scala
@@ -61,8 +61,8 @@ class FastqSyncTest extends TestNGSuite with MockitoSugar with Matchers {
val (numDiscard1, numDiscard2, numKept) = syncFastq(refMock, aMock, bMock, aOutMock, bOutMock)
- obs.verify(aOutMock).write(exp(0))
- obs.verify(bOutMock).write(exp(0))
+ obs.verify(aOutMock).write(exp.head)
+ obs.verify(bOutMock).write(exp.head)
obs.verify(aOutMock).write(exp(1))
obs.verify(bOutMock).write(exp(1))
@@ -156,8 +156,8 @@ class FastqSyncTest extends TestNGSuite with MockitoSugar with Matchers {
val (numDiscard1, numDiscard2, numKept) = syncFastq(refMock, aMock, bMock, aOutMock, bOutMock)
// exp(1) is discarded by syncFastq
- obs.verify(aOutMock).write(exp(0))
- obs.verify(bOutMock).write(exp(0))
+ obs.verify(aOutMock).write(exp.head)
+ obs.verify(bOutMock).write(exp.head)
obs.verify(aOutMock).write(exp(2))
obs.verify(bOutMock).write(exp(2))
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala
index 5a13cbed3ce6b29b0bf1a785cc46597499d695eb..d9180aec45025b68e9830227110ca9320571b683 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/SeqStatTest.scala
@@ -92,7 +92,7 @@ class SeqStatTest extends TestNGSuite with MockitoSugar with Matchers {
baseHistogram(39) shouldEqual 5
baseHistogram(34) shouldEqual 5
baseHistogram(33) shouldEqual 5
- baseHistogram(0) shouldEqual 5
+ baseHistogram.head shouldEqual 5
}
@Test def testArgsMinimum() = {
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
index 303fb0c2885fc4eb1553ce5bbb5b8ea794613871..3a5bc994c400466d6d11ceb491092fa61788bdd5 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
@@ -29,7 +29,7 @@ import scala.collection.mutable
class VcfStatsTest extends TestNGSuite with Matchers {
@Test
- def testSampleToSampleStats: Unit = {
+ def testSampleToSampleStats(): Unit = {
val s1 = SampleToSampleStats()
val s2 = SampleToSampleStats()
s1.alleleOverlap shouldBe 0
@@ -60,7 +60,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
}
@Test
- def testSampleStats: Unit = {
+ def testSampleStats(): Unit = {
val s1 = SampleStats()
val s2 = SampleStats()
@@ -94,7 +94,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
}
@Test
- def testAlleleOverlap: Unit = {
+ def testAlleleOverlap(): Unit = {
val a1 = Allele.create("G")
val a2 = Allele.create("A")
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
index cd727490481a3689bc0b4ddde5b6040ba412d48a..b2a063f9853c07ceb23f623b174e5d7980dc275f 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VepNormalizerTest.scala
@@ -92,21 +92,21 @@ class VepNormalizerTest extends TestNGSuite with MockitoSugar with Matchers {
val reader = new VCFFileReader(vepped, false)
val header = reader.getFileHeader
val new_infos = parseCsq(header)
- explodeTranscripts(reader.iterator().next(), new_infos, true).length should be(11)
+ explodeTranscripts(reader.iterator().next(), new_infos, removeCsq = true).length should be(11)
}
@Test def testStandardVEPLength() = {
val reader = new VCFFileReader(vepped, false)
val header = reader.getFileHeader
val new_infos = parseCsq(header)
- Array(standardTranscripts(reader.iterator().next(), new_infos, true)).length should be(1)
+ Array(standardTranscripts(reader.iterator().next(), new_infos, removeCsq = true)).length should be(1)
}
@Test def testStandardVEPAttributeLength() = {
val reader = new VCFFileReader(vepped, false)
val header = reader.getFileHeader
val new_infos = parseCsq(header)
- val record = standardTranscripts(reader.iterator().next(), new_infos, true)
+ val record = standardTranscripts(reader.iterator().next(), new_infos, removeCsq = true)
def checkItems(items: Array[String]) = {
items.foreach { check }
}
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala
index 616ef60e42ce4b83f1c29e8b81a23fd31224c26f..4b98bba0c873a0ec5aa9c48a51c36475280adbfb 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/WipeReadsTest.scala
@@ -195,7 +195,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
// and only filling the filter with a few items
val filterNotFunc = makeFilterNotFunction(intervals, sBamFile1, bloomSize = bloomSize, bloomFp = bloomFp)
// by default, set elements are SAM record read names
- filterNotFunc(sBamRecs1(0)) shouldBe false
+ filterNotFunc(sBamRecs1.head) shouldBe false
filterNotFunc(sBamRecs1(1)) shouldBe true
filterNotFunc(sBamRecs1(2)) shouldBe true
filterNotFunc(sBamRecs1(3)) shouldBe true
@@ -211,7 +211,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
new Interval("P", 191, 480)
)
val filterNotFunc = makeFilterNotFunction(intervals, sBamFile1, bloomSize = bloomSize, bloomFp = bloomFp)
- filterNotFunc(sBamRecs1(0)) shouldBe false
+ filterNotFunc(sBamRecs1.head) shouldBe false
filterNotFunc(sBamRecs1(1)) shouldBe true
filterNotFunc(sBamRecs1(2)) shouldBe true
filterNotFunc(sBamRecs1(3)) shouldBe true
@@ -225,7 +225,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
new Interval("chrQ", 881, 1000) // overlaps first exon of r05
)
val filterNotFunc = makeFilterNotFunction(intervals, sBamFile1, bloomSize = bloomSize, bloomFp = bloomFp)
- filterNotFunc(sBamRecs1(0)) shouldBe false
+ filterNotFunc(sBamRecs1.head) shouldBe false
filterNotFunc(sBamRecs1(1)) shouldBe false
filterNotFunc(sBamRecs1(2)) shouldBe false
filterNotFunc(sBamRecs1(3)) shouldBe false
@@ -240,7 +240,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
new Interval("chrQ", 900, 920)
)
val filterNotFunc = makeFilterNotFunction(intervals, sBamFile1, bloomSize = bloomSize, bloomFp = bloomFp)
- filterNotFunc(sBamRecs1(0)) shouldBe false
+ filterNotFunc(sBamRecs1.head) shouldBe false
filterNotFunc(sBamRecs1(1)) shouldBe false
filterNotFunc(sBamRecs1(2)) shouldBe false
filterNotFunc(sBamRecs1(3)) shouldBe false
@@ -256,7 +256,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
new Interval("chrR", 500, 505)
)
val filterNotFunc = makeFilterNotFunction(intervals, sBamFile5, bloomSize = bloomSize, bloomFp = bloomFp)
- filterNotFunc(sBamRecs5(0)) shouldBe true
+ filterNotFunc(sBamRecs5.head) shouldBe true
filterNotFunc(sBamRecs5(1)) shouldBe false
filterNotFunc(sBamRecs5(2)) shouldBe false
filterNotFunc(sBamRecs5(3)) shouldBe true
@@ -271,7 +271,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
)
val filterNotFunc = makeFilterNotFunction(intervals, sBamFile1, bloomSize = bloomSize, bloomFp = bloomFp,
filterOutMulti = false)
- filterNotFunc(sBamRecs1(0)) shouldBe false
+ filterNotFunc(sBamRecs1.head) shouldBe false
filterNotFunc(sBamRecs1(1)) shouldBe false
filterNotFunc(sBamRecs1(2)) shouldBe true
filterNotFunc(sBamRecs1(3)) shouldBe true
@@ -287,7 +287,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
)
val filterNotFunc = makeFilterNotFunction(intervals, sBamFile2, bloomSize = bloomSize, bloomFp = bloomFp,
minMapQ = 60)
- filterNotFunc(sBamRecs2(0)) shouldBe false
+ filterNotFunc(sBamRecs2.head) shouldBe false
// r01 is not in since it is below the MAPQ threshold
filterNotFunc(sBamRecs2(1)) shouldBe false
filterNotFunc(sBamRecs2(2)) shouldBe false
@@ -305,7 +305,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
)
val filterNotFunc = makeFilterNotFunction(intervals, sBamFile2, bloomSize = bloomSize, bloomFp = bloomFp,
minMapQ = 60, filterOutMulti = false)
- filterNotFunc(sBamRecs2(0)) shouldBe false
+ filterNotFunc(sBamRecs2.head) shouldBe false
filterNotFunc(sBamRecs2(1)) shouldBe false
// this r01 is not in since it is below the MAPQ threshold
filterNotFunc(sBamRecs2(2)) shouldBe false
@@ -324,7 +324,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
)
val filterNotFunc = makeFilterNotFunction(intervals, sBamFile2, bloomSize = bloomSize, bloomFp = bloomFp,
readGroupIds = Set("002", "003"))
- filterNotFunc(sBamRecs2(0)) shouldBe false
+ filterNotFunc(sBamRecs2.head) shouldBe false
// only r01 is in the set since it is RG 002
filterNotFunc(sBamRecs2(1)) shouldBe true
filterNotFunc(sBamRecs2(2)) shouldBe true
@@ -342,7 +342,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
new Interval("chrQ", 991, 1000) // overlaps nothing; lies in the spliced region of r05
)
val filterNotFunc = makeFilterNotFunction(intervals, pBamFile1, bloomSize = bloomSize, bloomFp = bloomFp)
- filterNotFunc(pBamRecs1(0)) shouldBe false
+ filterNotFunc(pBamRecs1.head) shouldBe false
filterNotFunc(pBamRecs1(1)) shouldBe false
filterNotFunc(pBamRecs1(2)) shouldBe true
filterNotFunc(pBamRecs1(3)) shouldBe true
@@ -363,7 +363,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
new Interval("chrQ", 891, 1000)
)
val filterNotFunc = makeFilterNotFunction(intervals, pBamFile1, bloomSize = bloomSize, bloomFp = bloomFp)
- filterNotFunc(pBamRecs1(0)) shouldBe false
+ filterNotFunc(pBamRecs1.head) shouldBe false
filterNotFunc(pBamRecs1(1)) shouldBe false
filterNotFunc(pBamRecs1(2)) shouldBe false
filterNotFunc(pBamRecs1(3)) shouldBe false
@@ -387,7 +387,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
)
val filterNotFunc = makeFilterNotFunction(intervals, pBamFile1, bloomSize = bloomSize, bloomFp = bloomFp,
filterOutMulti = false)
- filterNotFunc(pBamRecs1(0)) shouldBe false
+ filterNotFunc(pBamRecs1.head) shouldBe false
filterNotFunc(pBamRecs1(1)) shouldBe false
filterNotFunc(pBamRecs1(2)) shouldBe false
filterNotFunc(pBamRecs1(3)) shouldBe false
@@ -411,7 +411,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
val filterNotFunc = makeFilterNotFunction(intervals, pBamFile2, bloomSize = bloomSize, bloomFp = bloomFp,
minMapQ = 60)
// r01 is not in since it is below the MAPQ threshold
- filterNotFunc(pBamRecs2(0)) shouldBe false
+ filterNotFunc(pBamRecs2.head) shouldBe false
filterNotFunc(pBamRecs2(1)) shouldBe false
filterNotFunc(pBamRecs2(2)) shouldBe false
filterNotFunc(pBamRecs2(3)) shouldBe false
@@ -431,7 +431,7 @@ class WipeReadsTest extends TestNGSuite with MockitoSugar with Matchers {
val filterNotFunc = makeFilterNotFunction(intervals, pBamFile2, bloomSize = bloomSize, bloomFp = bloomFp,
readGroupIds = Set("002", "003"))
// only r01 is in the set since it is RG 002
- filterNotFunc(pBamRecs2(0)) shouldBe false
+ filterNotFunc(pBamRecs2.head) shouldBe false
filterNotFunc(pBamRecs2(1)) shouldBe false
filterNotFunc(pBamRecs2(2)) shouldBe true
filterNotFunc(pBamRecs2(3)) shouldBe true
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
index 6a8e8f225ccd2fdc72444bb2cc71bd730107f85d..dbb6b6faa920ff32f10288bccb6edb2410aab03d 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
@@ -31,7 +31,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
import ConfigUtils._
import ConfigUtilsTest._
- @Test def testGetValueFromPath: Unit = {
+ @Test def testGetValueFromPath(): Unit = {
getValueFromPath(map1, List("dummy")) shouldBe Some(Map("dummy" -> 1))
getValueFromPath(map1, List("dummy", "dummy")) shouldBe Some(1)
getValueFromPath(map1, List("nested3", "nested2", "nested1")) shouldBe Some(Map("dummy" -> 1))
@@ -39,7 +39,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
getValueFromPath(map1, List("dummy", "notexist")) shouldBe None
}
- @Test def testGetMapFromPath: Unit = {
+ @Test def testGetMapFromPath(): Unit = {
getMapFromPath(map1, List("dummy")) shouldBe Some(Map("dummy" -> 1))
getMapFromPath(map1, List("nested3", "nested2", "nested1")) shouldBe Some(Map("dummy" -> 1))
intercept[IllegalStateException] {
@@ -48,7 +48,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
}
// Merge maps
- @Test def testMergeMaps: Unit = {
+ @Test def testMergeMaps(): Unit = {
val mergedMap = mergeMaps(map1, map2)
getValueFromPath(mergedMap, List("nested", "1")) shouldBe Some(1)
getValueFromPath(mergedMap, List("nested", "2")) shouldBe Some(1)
@@ -56,7 +56,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
}
// Json to scala values
- @Test def testFileToJson: Unit = {
+ @Test def testFileToJson(): Unit = {
fileToJson(file1) shouldBe json1
fileToJson(file2) shouldBe json2
intercept[IllegalStateException] {
@@ -64,7 +64,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
}
}
- @Test def testJsonToMap: Unit = {
+ @Test def testJsonToMap(): Unit = {
jsonToMap(json1) shouldBe map1
jsonToMap(json2) shouldBe map2
intercept[IllegalStateException] {
@@ -72,13 +72,13 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
}
}
- @Test def testFileToConfigMap: Unit = {
+ @Test def testFileToConfigMap(): Unit = {
fileToConfigMap(file1) shouldBe map1
fileToConfigMap(file2) shouldBe map2
}
// Any/scala values to Json objects
- @Test def testAnyToJson: Unit = {
+ @Test def testAnyToJson(): Unit = {
anyToJson("bla") shouldBe jString("bla")
anyToJson(1337) shouldBe Json.jNumberOrString(1337)
anyToJson(13.37) shouldBe Json.jNumberOrString(13.37)
@@ -90,7 +90,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
anyToJson(Map("bla" -> 1337)) shouldBe ("bla" := 1337) ->: jEmptyObject
}
- @Test def testMapToJson: Unit = {
+ @Test def testMapToJson(): Unit = {
mapToJson(Map()) shouldBe jEmptyObject
mapToJson(Map("bla" -> 1337)) shouldBe ("bla" := 1337) ->: jEmptyObject
mapToJson(Map("bla" -> Map())) shouldBe ("bla" := jEmptyObject) ->: jEmptyObject
@@ -98,14 +98,14 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
}
// Any to scala values
- @Test def testAny2string: Unit = {
+ @Test def testAny2string(): Unit = {
any2string("bla") shouldBe "bla"
any2string(1337) shouldBe "1337"
any2string(true) shouldBe "true"
any2string(13.37) shouldBe "13.37"
}
- @Test def testAny2int: Unit = {
+ @Test def testAny2int(): Unit = {
any2int(1337) shouldBe 1337
any2int("1337") shouldBe 1337
any2int(13.37) shouldBe 13
@@ -114,7 +114,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
}
}
- @Test def testAny2long: Unit = {
+ @Test def testAny2long(): Unit = {
any2long(1337L) shouldBe 1337L
any2long(1337) shouldBe 1337L
any2long("1337") shouldBe 1337L
@@ -124,7 +124,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
}
}
- @Test def testAny2double: Unit = {
+ @Test def testAny2double(): Unit = {
any2double(13.37) shouldBe 13.37d
any2double("1337") shouldBe 1337d
any2double(1337) shouldBe 1337d
@@ -135,7 +135,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
}
}
- @Test def testAny2float: Unit = {
+ @Test def testAny2float(): Unit = {
any2float(1337d) shouldBe 1337f
any2float("1337") shouldBe 1337f
any2float(1337) shouldBe 1337f
@@ -146,7 +146,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
}
}
- @Test def testAny2boolean: Unit = {
+ @Test def testAny2boolean(): Unit = {
any2boolean(true) shouldBe true
any2boolean("false") shouldBe false
any2boolean("true") shouldBe true
@@ -157,21 +157,21 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
}
}
- @Test def testAny2list: Unit = {
+ @Test def testAny2list(): Unit = {
any2list(Nil) shouldBe Nil
any2list(List(1, 2, 3, 4)) shouldBe List(1, 2, 3, 4)
any2list(List(1337)) shouldBe List(1337)
any2list(1337) shouldBe List(1337)
}
- @Test def testAny2stringList: Unit = {
+ @Test def testAny2stringList(): Unit = {
any2stringList(Nil) shouldBe Nil
any2stringList(List("1337")) shouldBe List("1337")
any2stringList(List(1337)) shouldBe List("1337")
any2stringList(1337) shouldBe List("1337")
}
- @Test def testAny2map: Unit = {
+ @Test def testAny2map(): Unit = {
any2map(Map()) shouldBe Map()
any2map(Map("bla" -> 1337)) shouldBe Map("bla" -> 1337)
any2map(null) shouldBe null
@@ -180,7 +180,7 @@ class ConfigUtilsTest extends TestNGSuite with Matchers {
}
}
- @Test def testImplicits: Unit = {
+ @Test def testImplicits(): Unit = {
val index = ConfigValueIndex("test", Nil, "test")
new ImplicitConversions {
configValue2list(ConfigValue(index, index, List(""))) shouldBe List("")
@@ -210,7 +210,7 @@ object ConfigUtilsTest {
val w = new PrintWriter(file)
w.write(text)
w.close()
- return file
+ file
}
val jsonText1 =
diff --git a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala
index c12dbacdb7ff2fc1eccf80d1a15c7ffac3530d4e..4eeab2a8d6e0452787238053ce2ed88ac3cc7db5 100644
--- a/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala
+++ b/public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala
@@ -11,13 +11,13 @@ import scala.util.Try
*/
class PackageTest extends TestNGSuite with Matchers {
- @Test def testConvert: Unit = {
+ @Test def testConvert(): Unit = {
tryToParseNumber("4") shouldBe Try(4)
tryToParseNumber("13.37") shouldBe Try(13.37)
tryToParseNumber("I'm not a number") should not be Try("I'm not a number")
- tryToParseNumber("4", true) shouldBe Try(4)
- tryToParseNumber("13.37", true) shouldBe Try(13.37)
- tryToParseNumber("I'm not a number", true) shouldBe Try("I'm not a number")
+ tryToParseNumber("4", fallBack = true) shouldBe Try(4)
+ tryToParseNumber("13.37", fallBack = true) shouldBe Try(13.37)
+ tryToParseNumber("I'm not a number", fallBack = true) shouldBe Try("I'm not a number")
}
}