Merge branch 'tests-increase_utilcoverage' into 'develop'

Branch for adding tests to increase test coverage for tools and utils



See merge request !332

public/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/summary/WriteSummaryTest.scala

@@ -197,7 +197,7 @@ class WriteSummaryTest extends TestNGSuite with Matchers {
 
 object WriteSummaryTest {
   def makeWriter(root: Configurable, c: Map[String, Any] = Map()) = new WriteSummary(root) {
-    override def globalConfig = new Config(c)
+    override def globalConfig = new Config(c + ("exe" -> "test"))
     override def outputs = Seq()
     override def inputs = Seq()
     qSettings = new QSettings {
@@ -238,7 +238,7 @@ object WriteSummaryTest {
       libId = l
       summaryName = "test"
       outputDir = new File(".").getAbsoluteFile
-      override def globalConfig = new Config(c)
+      override def globalConfig = new Config(c + ("exe" -> "test"))
       def summarySettings: Map[String, Any] = settings
       def summaryFiles: Map[String, File] = files
       val tempFile = File.createTempFile("summary", ".json")
@@ -256,7 +256,7 @@ object WriteSummaryTest {
     new MultiSampleQScript with QScript {
       summaryName = "test"
       outputDir = new File(".").getAbsoluteFile
-      override def globalConfig = new Config(c)
+      override def globalConfig = new Config(c + ("exe" -> "test"))
       def summarySettings: Map[String, Any] = settings
       def summaryFiles: Map[String, File] = files
       val tempFile = File.createTempFile("summary", ".json")

public/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/BamUtilsTest.scala

@@ -31,15 +31,37 @@ class BamUtilsTest extends TestNGSuite with MockitoSugar with Matchers {
     new SAMLineParser(samh)
   }
 
-  private def makeSams(raws: String*): Seq[SAMRecord] =
-    raws.map(s => samHeaderTemplate.parseLine(s))
+  private val samHeaderTemplateDoubleSample: SAMLineParser = {
+    val samh = new SAMFileHeader
+    samh.setSortOrder(SAMFileHeader.SortOrder.coordinate)
+    samh.addSequence(new SAMSequenceRecord("chrQ", 10000))
+    samh.addSequence(new SAMSequenceRecord("chrR", 10000))
+    val readGroup1 = new SAMReadGroupRecord("001")
+    readGroup1.setSample("sampleX")
+    samh.addReadGroup(readGroup1)
+    val readGroup2 = new SAMReadGroupRecord("002")
+    readGroup2.setSample("sampleY")
+    samh.addReadGroup(readGroup2)
+    new SAMLineParser(samh)
+  }
+
+  private val samHeaderTemplateErrornousNoReadgroup: SAMLineParser = {
+    val samh = new SAMFileHeader
+    samh.setSortOrder(SAMFileHeader.SortOrder.coordinate)
+    samh.addSequence(new SAMSequenceRecord("chrQ", 10000))
+    samh.addSequence(new SAMSequenceRecord("chrR", 10000))
+    new SAMLineParser(samh)
+  }
+
+  private def makeSams(header: SAMLineParser, raws: Seq[String]): Seq[SAMRecord] =
+    raws.map(s => header.parseLine(s))
 
   private def makeSamReader(f: File): SamReader = SamReaderFactory
     .make()
     .validationStringency(ValidationStringency.LENIENT)
     .open(f)
 
-  val sBamRecs1 = makeSams(
+  val sBamRecs1 = Seq(
     "r02\t0\tchrQ\t50\t60\t10M\t*\t0\t0\tTACGTACGTA\tEEFFGGHHII\tRG:Z:001",
     "r01\t16\tchrQ\t190\t60\t10M\t*\t0\t0\tTACGTACGTA\tEEFFGGHHII\tRG:Z:001",
     "r01\t16\tchrQ\t290\t60\t10M\t*\t0\t0\tGGGGGAAAAA\tGGGGGGGGGG\tRG:Z:001",
@@ -49,7 +71,12 @@ class BamUtilsTest extends TestNGSuite with MockitoSugar with Matchers {
     "r06\t4\t*\t0\t0\t*\t*\t0\t0\tATATATATAT\tHIHIHIHIHI\tRG:Z:001"
   )
 
-  val pBamRecs1 = makeSams(
+  val sBamRecs2 = Seq(
+    "r02\t0\tchrQ\t50\t60\t10M\t*\t0\t0\tTACGTACGTA\tEEFFGGHHII\t",
+    "r01\t16\tchrQ\t190\t60\t10M\t*\t0\t0\tTACGTACGTA\tEEFFGGHHII\t"
+  )
+
+  val pBamRecs1 = Seq(
     "r02\t99\tchrQ\t50\t60\t10M\t=\t90\t50\tTACGTACGTA\tEEFFGGHHII\tRG:Z:001",
     "r02\t147\tchrQ\t90\t60\t10M\t=\t50\t-50\tATGCATGCAT\tEEFFGGHHII\tRG:Z:001",
     "r01\t163\tchrQ\t150\t60\t10M\t=\t190\t50\tAAAAAGGGGG\tGGGGGGGGGG\tRG:Z:001",
@@ -66,18 +93,32 @@ class BamUtilsTest extends TestNGSuite with MockitoSugar with Matchers {
     "r06\t4\t*\t0\t0\t*\t*\t0\t0\tGCGCGCGCGC\tHIHIHIHIHI\tRG:Z:001"
   )
 
+  val pBamRecs2 = Seq(
+    "r01\t163\tchrQ\t150\t60\t10M\t=\t190\t50\tAAAAAGGGGG\tGGGGGGGGGG\t",
+    "r01\t83\tchrQ\t190\t60\t10M\t=\t150\t-50\tGGGGGAAAAA\tGGGGGGGGGG\t",
+    "r01\t163\tchrQ\t250\t60\t10M\t=\t290\t50\tAAAAAGGGGG\tGGGGGGGGGG\t",
+    "r01\t83\tchrQ\t290\t60\t10M\t=\t250\t-50\tGGGGGAAAAA\tGGGGGGGGGG\t"
+  )
+
   @BeforeClass
   def start: Unit = {
-    createTestFileFrom(sBamRecs1, BamUtilsTest.singleEndBam01)
-    createTestFileFrom(pBamRecs1, BamUtilsTest.pairedEndBam01)
+    createTestFileFrom(makeSams(samHeaderTemplate, sBamRecs1), samHeaderTemplate, BamUtilsTest.singleEndBam01)
+    createTestFileFrom(makeSams(samHeaderTemplate, pBamRecs1), samHeaderTemplate, BamUtilsTest.pairedEndBam01)
+    createTestFileFrom(makeSams(samHeaderTemplate, pBamRecs1), samHeaderTemplate, BamUtilsTest.pairedEndBam02)
+
+    createTestFileFrom(makeSams(samHeaderTemplateDoubleSample, sBamRecs1), samHeaderTemplateDoubleSample, BamUtilsTest.singleEndBam01WithDoubleSamples)
+    createTestFileFrom(makeSams(samHeaderTemplateDoubleSample, pBamRecs1), samHeaderTemplateDoubleSample, BamUtilsTest.pairedEndBam01WithDoubleSamples)
+
+    createTestFileFrom(makeSams(samHeaderTemplateErrornousNoReadgroup, sBamRecs2), samHeaderTemplateErrornousNoReadgroup, BamUtilsTest.singleEndBam01NoRG)
+    createTestFileFrom(makeSams(samHeaderTemplateErrornousNoReadgroup, pBamRecs2), samHeaderTemplateErrornousNoReadgroup, BamUtilsTest.pairedEndBam01NoRG)
   }
 
-  private def createTestFileFrom(records: Seq[SAMRecord], output: File): File = {
+  private def createTestFileFrom(records: Seq[SAMRecord], header: SAMLineParser, output: File): File = {
     output.getParentFile.createNewFile()
     val outBam = new SAMFileWriterFactory()
       .setCreateIndex(true)
       .setUseAsyncIo(true)
-      .makeBAMWriter(samHeaderTemplate.getFileHeader, true, output)
+      .makeBAMWriter(header.getFileHeader, true, output)
     writeBam(records, outBam)
     output
   }
@@ -132,6 +173,40 @@ class BamUtilsTest extends TestNGSuite with MockitoSugar with Matchers {
     )
   }
 
+  @Test def testSampleBamNamesMultipleSamplesSE = {
+    val thrown = intercept[IllegalArgumentException] {
+      sampleBamMap(List(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)
+  }
+
+  @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)
+  }
+
+  @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)
+  }
+
+  @Test def testSampleFoundTwice = {
+    val thrown = intercept[IllegalArgumentException] {
+      sampleBamMap(List(BamUtilsTest.pairedEndBam01, BamUtilsTest.pairedEndBam02))
+    }
+    thrown.getMessage should ===("Samples has been found twice")
+  }
 }
 
 object BamUtilsTest {
@@ -139,4 +214,16 @@ object BamUtilsTest {
   singleEndBam01.deleteOnExit()
   var pairedEndBam01: File = File.createTempFile("bamutils", "paired01.bam")
   singleEndBam01.deleteOnExit()
-}
\ No newline at end of file
+  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")
+  pairedEndBam01WithDoubleSamples.deleteOnExit()
+
+  var singleEndBam01NoRG: File = File.createTempFile("bamutils", "single01norg.bam")
+  singleEndBam01NoRG.deleteOnExit()
+  var pairedEndBam01NoRG: File = File.createTempFile("bamutils", "paired01norg.bam")
+  singleEndBam01NoRG.deleteOnExit()
+}