diff --git a/bam2wig/pom.xml b/bam2wig/pom.xml
index 5afb29d42f96f6bda92b4d8c6a35d2b09308f558..82fc7fff5fd91f4c46fd22421fdb54c89ccf3871 100644
--- a/bam2wig/pom.xml
+++ b/bam2wig/pom.xml
@@ -45,6 +45,18 @@
<artifactId>BiopetExtensions</artifactId>
<version>${project.version}</version>
</dependency>
+ <dependency>
+ <groupId>org.scalatest</groupId>
+ <artifactId>scalatest_2.10</artifactId>
+ <version>2.2.1</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.testng</groupId>
+ <artifactId>testng</artifactId>
+ <version>6.8</version>
+ <scope>test</scope>
+ </dependency>
</dependencies>
</project>
\ No newline at end of file
diff --git a/bam2wig/src/test/resources/empty.bam b/bam2wig/src/test/resources/empty.bam
new file mode 100644
index 0000000000000000000000000000000000000000..bd4073d80cbf73c689e97d2814f9b1fd00d63895
Binary files /dev/null and b/bam2wig/src/test/resources/empty.bam differ
diff --git a/bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala b/bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..eaf2ae37a5d844ba93669f2fef4f0a5d98ab962d
--- /dev/null
+++ b/bam2wig/src/test/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizesTest.scala
@@ -0,0 +1,30 @@
+package nl.lumc.sasc.biopet.pipelines.bamtobigwig
+
+import java.io.File
+import java.nio.file.Paths
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.io.Source
+
+/**
+ * Created by pjvanthof on 09/05/16.
+ */
+class BamToChromSizesTest extends TestNGSuite with Matchers {
+ private def resourcePath(p: String): String = {
+ Paths.get(getClass.getResource(p).toURI).toString
+ }
+
+ @Test
+ def testChromSizes: Unit = {
+ val bamFile = new File(resourcePath("/empty.bam"))
+ val bamToChromSizes = new BamToChromSizes(null)
+ bamToChromSizes.bamFile = bamFile
+ bamToChromSizes.chromSizesFile = File.createTempFile("chrom.", ".sizes")
+ bamToChromSizes.chromSizesFile.deleteOnExit()
+ bamToChromSizes.run()
+ Source.fromFile(bamToChromSizes.chromSizesFile).getLines().toList shouldBe List("chrQ\t10000", "chrR\t10000")
+ }
+}
diff --git a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
index a43cb3890bcf3521e3be6645b4e175c59f84d143..529e6830db48b454499a7344c8606229669acab9 100644
--- a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
+++ b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/WriteDependencies.scala
@@ -30,18 +30,16 @@ import scala.collection.mutable.ListBuffer
*/
object WriteDependencies extends Logging with Configurable {
val root: Configurable = null
- private val functionNames: mutable.Map[QFunction, String] = mutable.Map()
-
- private def createFunctionNames(functions: Seq[QFunction]): Unit = {
+ private def createFunctionNames(functions: Seq[QFunction]): Map[QFunction, String] = {
val cache: mutable.Map[String, Int] = mutable.Map()
- for (function <- functions) {
+ (for (function <- functions) yield {
val baseName = function match {
case f: Configurable => f.configNamespace
case f => f.getClass.getSimpleName
}
cache += baseName -> (cache.getOrElse(baseName, 0) + 1)
- functionNames += function -> s"$baseName-${cache(baseName)}"
- }
+ function -> s"$baseName-${cache(baseName)}"
+ }).toMap
}
/**
@@ -55,7 +53,7 @@ object WriteDependencies extends Logging with Configurable {
val errorOnMissingInput: Boolean = config("error_on_missing_input", false)
- createFunctionNames(functions)
+ val functionNames = createFunctionNames(functions)
case class QueueFile(file: File) {
private val inputJobs: ListBuffer[QFunction] = ListBuffer()
diff --git a/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala b/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..b8dee445d737323893c1f5a85dce8b75f7feec72
--- /dev/null
+++ b/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/WriteDependenciesTest.scala
@@ -0,0 +1,60 @@
+package nl.lumc.sasc.biopet.core
+
+import java.io.File
+import java.nio.file.Files
+
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.broadinstitute.gatk.queue.function.QFunction
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.io.Source
+
+/**
+ * Created by pjvanthof on 09/05/16.
+ */
+class WriteDependenciesTest extends TestNGSuite with Matchers {
+
+ import WriteDependenciesTest._
+
+ case class Qfunc(in: Seq[File], out: Seq[File]) extends QFunction {
+ override def inputs = in
+ override def outputs = out
+ override def doneOutputs = out.map(x => new File(x.getParentFile, s".${x.getName}.done"))
+ override def failOutputs = out.map(x => new File(x.getParentFile, s".${x.getName}.fail"))
+ jobOutputFile = new File(out.head + ".out")
+ }
+
+ @Test
+ def testDeps: Unit = {
+ val outputFile = File.createTempFile("deps.", ".json")
+ outputFile.deleteOnExit()
+ val func1 = Qfunc(file1 :: Nil, file2 :: Nil)
+ val func2 = Qfunc(file2 :: Nil, file3 :: Nil)
+ WriteDependencies.writeDependencies(func1 :: func2 :: Nil, outputFile)
+ val deps = ConfigUtils.fileToConfigMap(outputFile)
+ deps("jobs") shouldBe a[Map[_, _]]
+ val jobs = deps("jobs").asInstanceOf[Map[String, Map[String, Any]]]
+ jobs.count(_._1.contains("Qfunc")) shouldBe 2
+
+ deps("files") shouldBe a[List[_]]
+ val files = deps("files").asInstanceOf[List[Map[String, Any]]]
+ val paths = files.map(x => x.get("path")).flatten
+ assert(paths.contains(file1.toString))
+ assert(paths.contains(file2.toString))
+ assert(paths.contains(file3.toString))
+
+ files.find(_.get("path") == Some(file1.toString)).flatMap(_.get("pipeline_input")) shouldBe Some(true)
+ files.find(_.get("path") == Some(file2.toString)).flatMap(_.get("pipeline_input")) shouldBe Some(false)
+ files.find(_.get("path") == Some(file3.toString)).flatMap(_.get("pipeline_input")) shouldBe Some(false)
+ }
+}
+
+object WriteDependenciesTest {
+ val tempDir = Files.createTempDirectory("test").toFile
+ tempDir.deleteOnExit()
+ val file1 = new File(tempDir, "file1.txt")
+ val file2 = new File(tempDir, "file2.txt")
+ val file3 = new File(tempDir, "file3.txt")
+}
\ No newline at end of file
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
index ed0065e589e17000a4e4fb9742d4bca71f6622a1..1460f3f6de300d2fed31e573d7d9ea49aa77d854 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
@@ -69,7 +69,7 @@ class CombineGVCFs(val root: Configurable) extends CommandLineGATK with ScatterG
override def cmdLine = super.cmdLine +
repeat("-A", annotation, spaceSeparated = true, escape = true, format = "%s") +
repeat("-G", group, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
repeat("-V", variant, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
conditional(convertToBasePairResolution, "-bpResolution", escape = true, format = "%s") +
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
index 650340d63c1be0ba9195609a616ddddb4abee8ef..ac939b07842e301928a4daf5d9528318b9595bf5 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
@@ -106,16 +106,12 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
@Gather(enabled = false)
private var outputIndex: File = _
- @Output
- @Gather(enabled = false)
- private var dbsnpIndex: File = _
-
override def beforeGraph() {
super.beforeGraph()
deps ++= variant.filter(orig => orig != null && (!orig.getName.endsWith(".list"))).map(orig => VcfUtils.getVcfIndexFile(orig))
if (out != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(out))
outputIndex = VcfUtils.getVcfIndexFile(out)
- dbsnp.foreach(x => dbsnpIndex = VcfUtils.getVcfIndexFile(x))
+ dbsnp.foreach(x => deps :+= VcfUtils.getVcfIndexFile(x))
}
override def cmdLine = super.cmdLine +
@@ -133,7 +129,7 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") +
repeat("-A", annotation, spaceSeparated = true, escape = true, format = "%s") +
repeat("-G", group, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
conditional(filter_reads_with_N_cigar, "-filterRNC", escape = true, format = "%s") +
conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s")
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
index 9eac2ba9e3d4974e7b479addcb3d0f1dadf5ef56..403bee79fea30f6ec521ce9dd36927be745f8640 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
@@ -419,7 +419,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
optional("-likelihoodEngine", likelihoodCalculationEngine, spaceSeparated = true, escape = true, format = "%s") +
optional("-hksr", heterogeneousKmerSizeResolution, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
conditional(dontTrimActiveRegions, "-dontTrimActiveRegions", escape = true, format = "%s") +
optional("-maxDiscARExtension", maxDiscARExtension, spaceSeparated = true, escape = true, format = "%s") +
optional("-maxGGAARExtension", maxGGAARExtension, spaceSeparated = true, escape = true, format = "%s") +
@@ -444,7 +444,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
repeat("-inputPrior", input_prior, spaceSeparated = true, escape = true, format = "%s") +
optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") +
optional("-gt_mode", genotyping_mode, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-alleles", alleles), alleles, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-alleles", alleles.getOrElse(null)), alleles, spaceSeparated = true, escape = true, format = "%s") +
optional("-contamination", contamination_fraction_to_filter, spaceSeparated = true, escape = true, format = contamination_fraction_to_filterFormat) +
optional("-contaminationFile", contamination_fraction_per_sample_file, spaceSeparated = true, escape = true, format = "%s") +
optional("-pnrm", p_nonref_model, spaceSeparated = true, escape = true, format = "%s") +
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
index a1ed7b732f9b72d1660c9ea8c1995e5fc0137a68..37885ac9c1958635d532e4ad2fc70ee5b9817cfb 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
@@ -218,8 +218,8 @@ class SelectVariants(val root: Configurable) extends CommandLineGATK with Scatte
override def cmdLine = super.cmdLine +
required(TaggedFile.formatCommandLineParameter("-V", variant), variant, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-disc", discordance), discordance, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-conc", concordance), concordance, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-disc", discordance.getOrElse(null)), discordance, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-conc", concordance.getOrElse(null)), concordance, spaceSeparated = true, escape = true, format = "%s") +
optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
repeat("-sn", sample_name, spaceSeparated = true, escape = true, format = "%s") +
repeat("-se", sample_expressions, spaceSeparated = true, escape = true, format = "%s") +
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
index 0edfe5260fe2fb9101fd92d01fbcebce94ba0441..42daf5e64018c1c8c51582cb3f2bbf9844bf1e37 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
@@ -276,7 +276,7 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
conditional(ignoreSNPAlleles, "-ignoreSNPAlleles", escape = true, format = "%s") +
conditional(allReadsSP, "-dl", escape = true, format = "%s") +
conditional(ignoreLaneInfo, "-ignoreLane", escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-referenceCalls", reference_sample_calls), reference_sample_calls, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-referenceCalls", reference_sample_calls.getOrElse(null)), reference_sample_calls, spaceSeparated = true, escape = true, format = "%s") +
optional("-refsample", reference_sample_name, spaceSeparated = true, escape = true, format = "%s") +
optional("-minqs", min_quality_score, spaceSeparated = true, escape = true, format = "%s") +
optional("-maxqs", max_quality_score, spaceSeparated = true, escape = true, format = "%s") +
@@ -291,14 +291,14 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
repeat("-inputPrior", input_prior, spaceSeparated = true, escape = true, format = "%s") +
optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") +
optional("-gt_mode", genotyping_mode, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-alleles", alleles), alleles, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-alleles", alleles.getOrElse(null)), alleles, spaceSeparated = true, escape = true, format = "%s") +
optional("-contamination", contamination_fraction_to_filter, spaceSeparated = true, escape = true, format = contamination_fraction_to_filterFormat) +
optional("-contaminationFile", contamination_fraction_per_sample_file, spaceSeparated = true, escape = true, format = "%s") +
optional("-pnrm", p_nonref_model, spaceSeparated = true, escape = true, format = "%s") +
optional("-logExactCalls", exactcallslog, spaceSeparated = true, escape = true, format = "%s") +
optional("-out_mode", output_mode, spaceSeparated = true, escape = true, format = "%s") +
conditional(allSitePLs, "-allSitePLs", escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
repeat("-comp", comp, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
repeat("-onlyEmitSamples", onlyEmitSamples, spaceSeparated = true, escape = true, format = "%s") +
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
index d98a55a49eb6e34c00588fddde66dc00cddfe610..0e35d9b81050cddd8d762e340c2f984bdd9c59ec 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
@@ -104,8 +104,8 @@ class VariantAnnotator(val root: Configurable) extends CommandLineGATK with Scat
override def cmdLine = super.cmdLine +
required(TaggedFile.formatCommandLineParameter("-V", variant), variant, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-snpEffFile", snpEffFile), snpEffFile, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-snpEffFile", snpEffFile.getOrElse()), snpEffFile, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse()), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
repeat("-comp", comp, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
repeat("-resource", resource, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
index cf1c362c7dd06b2eec25104fdfd3fb5a06dea2f8..182007076b311d97ff8c58e404eb498bc0f2b90b 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
@@ -135,8 +135,8 @@ class VariantEval(val root: Configurable) extends CommandLineGATK {
optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
repeat("-eval", eval, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
repeat("-comp", comp, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-gold", goldStandard), goldStandard, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-gold", goldStandard.getOrElse(null)), goldStandard, spaceSeparated = true, escape = true, format = "%s") +
repeat("-select", select_exps, spaceSeparated = true, escape = true, format = "%s") +
repeat("-selectName", select_names, spaceSeparated = true, escape = true, format = "%s") +
repeat("-sn", sample, spaceSeparated = true, escape = true, format = "%s") +
diff --git a/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala b/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala
index 6b863f81d16d4f26754ea87ddf5c703f35fd4588..301fdf1f31bb8475c1092fb76b69e2c667448ec1 100644
--- a/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala
+++ b/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/Summary.scala
@@ -61,7 +61,7 @@ class Summary(file: File) {
}
/** Executes given function for each sample */
- def getSampleValues(function: (Summary, String) => Option[Any]): Map[String, Option[Any]] = {
+ def getSampleValues[T](function: (Summary, String) => Option[T]): Map[String, Option[T]] = {
(for (sample <- samples) yield sample -> function(this, sample)).toMap
}
@@ -95,7 +95,7 @@ class Summary(file: File) {
* @param function Function to execute
* @return (sampleId, libId) -> value
*/
- def getLibraryValues(function: (Summary, String, String) => Option[Any]): Map[(String, String), Option[Any]] = {
+ def getLibraryValues[T](function: (Summary, String, String) => Option[T]): Map[(String, String), Option[T]] = {
(for (sample <- samples; lib <- libraries.getOrElse(sample, Set())) yield {
(sample, lib) -> function(this, sample, lib)
}).toMap
diff --git a/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/SummaryValue.scala b/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/SummaryValue.scala
index dbce03915e2ed8512e9e737f9189147670b76a5e..9ad67419137321027aceaa14a88781a32c74f0ff 100644
--- a/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/SummaryValue.scala
+++ b/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/SummaryValue.scala
@@ -33,7 +33,6 @@ case class SummaryValue(value: Option[Any]) {
})
}
- //TODO: Calculations are not yet used somewhere, needs more testing
def +(that: SummaryValue): SummaryValue = {
(this.value, that.value) match {
case (Some(a: Double), Some(b)) => SummaryValue(Some(a + b.toString.toDouble))
diff --git a/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/IoUtilsTest.scala b/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/IoUtilsTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..cd319fee6bcb0da8bccb7a1c474f1c566ab0dab5
--- /dev/null
+++ b/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/IoUtilsTest.scala
@@ -0,0 +1,81 @@
+package nl.lumc.sasc.biopet.utils
+
+import java.io.{ File, FileNotFoundException, PrintWriter }
+import java.nio.file.Files
+
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+import scala.io.Source
+
+/**
+ * Created by pjvanthof on 05/05/16.
+ */
+class IoUtilsTest extends TestNGSuite with Matchers {
+
+ def createTempTestFile(file: File): Unit = {
+ file.getParentFile.mkdirs()
+ val writer = new PrintWriter(file)
+ writer.println("test")
+ writer.close()
+ file.deleteOnExit()
+ }
+
+ @Test
+ def testCopyFile: Unit = {
+ val temp1 = File.createTempFile("test.", ".txt")
+ temp1.deleteOnExit()
+ val temp2 = File.createTempFile("test.", ".txt")
+ temp2.deleteOnExit()
+ createTempTestFile(temp1)
+ IoUtils.copyFile(temp1, temp2)
+ val reader = Source.fromFile(temp2)
+ reader.getLines().toList shouldBe List("test")
+ reader.close()
+ }
+
+ @Test
+ def testCopyFileNonExistingDir: Unit = {
+ val temp1 = File.createTempFile("test.", ".txt")
+ val tempDir = new File(Files.createTempDirectory("test").toFile, "non-exist")
+ tempDir.deleteOnExit()
+ tempDir shouldNot exist
+ val temp2 = new File(tempDir, "test.txt")
+ createTempTestFile(temp1)
+ intercept[FileNotFoundException] {
+ IoUtils.copyFile(temp1, temp2)
+ }
+ IoUtils.copyFile(temp1, temp2, true)
+ val reader = Source.fromFile(temp2)
+ reader.getLines().toList shouldBe List("test")
+ reader.close()
+ }
+
+ @Test
+ def testCopyDir: Unit = {
+ val tempDir1 = Files.createTempDirectory("test").toFile
+ tempDir1.deleteOnExit()
+ val tempDir2 = Files.createTempDirectory("test").toFile
+ tempDir2.deleteOnExit()
+ val relativePaths: List[String] = List(
+ "test1.txt",
+ "test2.txt",
+ "dir1" + File.separator + "test1.txt",
+ "dir1" + File.separator + "test2.txt",
+ "dir2" + File.separator + "test1.txt",
+ "dir2" + File.separator + "test2.txt")
+ relativePaths.foreach { x =>
+ createTempTestFile(new File(tempDir1, x))
+ new File(tempDir2, x) shouldNot exist
+ }
+ IoUtils.copyDir(tempDir1, tempDir2)
+ relativePaths.foreach { x =>
+ val file = new File(tempDir2, x)
+ file should exist
+ val reader = Source.fromFile(file)
+ reader.getLines().toList shouldBe List("test")
+ reader.close()
+ }
+ }
+}
diff --git a/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/SummaryTest.scala b/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/SummaryTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..45f650496cfa4e04784c4b4a9748d5b6ab18be5f
--- /dev/null
+++ b/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/SummaryTest.scala
@@ -0,0 +1,96 @@
+package nl.lumc.sasc.biopet.utils.summary
+
+import java.io.{ File, PrintWriter }
+
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvanthof on 06/05/16.
+ */
+class SummaryTest extends TestNGSuite with Matchers {
+ @Test
+ def testSamples: Unit = {
+ val summary = new Summary(SummaryTest.testSummaryFile)
+ summary.samples shouldBe Set("sample1")
+ }
+
+ @Test
+ def testLibraries: Unit = {
+ val summary = new Summary(SummaryTest.testSummaryFile)
+ summary.libraries shouldBe Map("sample1" -> Set("lib1"))
+ }
+
+ @Test
+ def testValue: Unit = {
+ val summary = new Summary(SummaryTest.testSummaryFile)
+ summary.getValue("key_1") shouldBe Some("test_1")
+ summary.getValue("key_x") shouldBe None
+ summary.getValue("samples", "sample1", "key_2") shouldBe Some("test_2")
+ summary.getValue("samples", "sample1", "libraries", "lib1", "key_3") shouldBe Some("test_3")
+
+ summary.getValue(Some("sample1"), None, "key_2") shouldBe Some("test_2")
+ summary.getValue(Some("sample1"), None, "key_x") shouldBe None
+ summary.getValue(Some("sample1"), Some("lib1"), "key_3") shouldBe Some("test_3")
+ summary.getValue(Some("sample1"), Some("lib1"), "key_x") shouldBe None
+ summary.getValue(None, None, "key_1") shouldBe Some("test_1")
+ summary.getValue(None, None, "key_x") shouldBe None
+ }
+
+ @Test
+ def testSampleValue: Unit = {
+ val summary = new Summary(SummaryTest.testSummaryFile)
+ summary.getSampleValue("sample1", "key_2") shouldBe Some("test_2")
+ summary.getSampleValue("sample1", "key_x") shouldBe None
+ summary.getSampleValue("samplex", "key_x") shouldBe None
+ }
+
+ @Test
+ def testSampleValues: Unit = {
+ val summary = new Summary(SummaryTest.testSummaryFile)
+ summary.getSampleValues("key_2") shouldBe Map("sample1" -> Some("test_2"))
+ summary.getSampleValues("key_x") shouldBe Map("sample1" -> None)
+ summary.getSampleValues((summary, sample) => summary.getSampleValue(sample, "key_2")) shouldBe Map("sample1" -> Some("test_2"))
+
+ }
+
+ @Test
+ def testLibraryValue: Unit = {
+ val summary = new Summary(SummaryTest.testSummaryFile)
+ summary.getLibraryValue("sample1", "lib1", "key_3") shouldBe Some("test_3")
+ summary.getLibraryValue("sample1", "lib1", "key_x") shouldBe None
+ summary.getLibraryValue("samplex", "libx", "key_x") shouldBe None
+ }
+
+ @Test
+ def testLibraryValues: Unit = {
+ val summary = new Summary(SummaryTest.testSummaryFile)
+ summary.getLibraryValues("key_3") shouldBe Map(("sample1", "lib1") -> Some("test_3"))
+ summary.getLibraryValues("key_x") shouldBe Map(("sample1", "lib1") -> None)
+ summary.getLibraryValues((summary, sample, lib) => summary.getLibraryValue(sample, lib, "key_3")) shouldBe Map(("sample1", "lib1") -> Some("test_3"))
+ }
+
+}
+
+object SummaryTest {
+ val testSummary = Map(
+ "key_1" -> "test_1",
+ "samples" -> Map(
+ "sample1" -> Map(
+ "key_2" -> "test_2",
+ "libraries" -> Map(
+ "lib1" -> Map("key_3" -> "test_3")
+ )
+ )
+ )
+ )
+
+ val testSummaryFile = File.createTempFile("summary.", ".json")
+ testSummaryFile.deleteOnExit()
+
+ val writer = new PrintWriter(testSummaryFile)
+ writer.println(ConfigUtils.mapToJson(testSummary).nospaces)
+ writer.close()
+}
diff --git a/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/SummaryValueTest.scala b/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/SummaryValueTest.scala
new file mode 100644
index 0000000000000000000000000000000000000000..f2996d522025debf22430cffdc3feae29e7b0737
--- /dev/null
+++ b/biopet-utils/src/test/scala/nl/lumc/sasc/biopet/utils/summary/SummaryValueTest.scala
@@ -0,0 +1,95 @@
+package nl.lumc.sasc.biopet.utils.summary
+
+import java.io.{ File, PrintWriter }
+
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import org.scalatest.Matchers
+import org.scalatest.testng.TestNGSuite
+import org.testng.annotations.Test
+
+/**
+ * Created by pjvanthof on 06/05/16.
+ */
+class SummaryValueTest extends TestNGSuite with Matchers {
+ @Test
+ def testConstructor: Unit = {
+ val summary = new Summary(SummaryValueTest.testSummaryFile)
+ new SummaryValue(None).value shouldBe None
+ new SummaryValue(Some(1)).value shouldBe Some(1)
+ new SummaryValue(List("key_1"), summary, None, None).value shouldBe Some("test_1")
+ new SummaryValue(List("key_2"), summary, Some("sample1"), None).value shouldBe Some("test_2")
+ new SummaryValue(List("key_3"), summary, Some("sample1"), Some("lib1")).value shouldBe Some("test_3")
+ }
+
+ @Test
+ def testPlus: Unit = {
+ new SummaryValue(Some(1.0)) + new SummaryValue(Some(1.0)) shouldBe new SummaryValue(Some(2.0))
+ new SummaryValue(Some(1.0)) + new SummaryValue(Some(1)) shouldBe new SummaryValue(Some(2.0))
+ new SummaryValue(Some(1)) + new SummaryValue(Some(1)) shouldBe new SummaryValue(Some(2))
+ new SummaryValue(Some("1")) + new SummaryValue(Some(1)) shouldBe new SummaryValue(Some(2.0))
+ new SummaryValue(Some("1")) + new SummaryValue(Some(1.0)) shouldBe new SummaryValue(Some(2.0))
+ new SummaryValue(None) + new SummaryValue(Some(1.0)) shouldBe new SummaryValue(None)
+ }
+
+ @Test
+ def testMin: Unit = {
+ new SummaryValue(Some(1.0)) - new SummaryValue(Some(1.0)) shouldBe new SummaryValue(Some(0.0))
+ new SummaryValue(Some(1.0)) - new SummaryValue(Some(1)) shouldBe new SummaryValue(Some(0.0))
+ new SummaryValue(Some(1)) - new SummaryValue(Some(1)) shouldBe new SummaryValue(Some(0))
+ new SummaryValue(Some("1")) - new SummaryValue(Some(1)) shouldBe new SummaryValue(Some(0.0))
+ new SummaryValue(Some("1")) - new SummaryValue(Some(1.0)) shouldBe new SummaryValue(Some(0.0))
+ new SummaryValue(None) - new SummaryValue(Some(1.0)) shouldBe new SummaryValue(None)
+ }
+
+ @Test
+ def testMultiply: Unit = {
+ new SummaryValue(Some(1.0)) * new SummaryValue(Some(2.0)) shouldBe new SummaryValue(Some(2.0))
+ new SummaryValue(Some(1.0)) * new SummaryValue(Some(2)) shouldBe new SummaryValue(Some(2.0))
+ new SummaryValue(Some(1)) * new SummaryValue(Some(2)) shouldBe new SummaryValue(Some(2))
+ new SummaryValue(Some("1")) * new SummaryValue(Some(2)) shouldBe new SummaryValue(Some(2.0))
+ new SummaryValue(Some("1")) * new SummaryValue(Some(2.0)) shouldBe new SummaryValue(Some(2.0))
+ new SummaryValue(None) * new SummaryValue(Some(2.0)) shouldBe new SummaryValue(None)
+ }
+
+ @Test
+ def testDivide: Unit = {
+ new SummaryValue(Some(2.0)) / new SummaryValue(Some(1.0)) shouldBe new SummaryValue(Some(2.0))
+ new SummaryValue(Some(2.0)) / new SummaryValue(Some(1)) shouldBe new SummaryValue(Some(2.0))
+ new SummaryValue(Some(2)) / new SummaryValue(Some(1)) shouldBe new SummaryValue(Some(2))
+ new SummaryValue(Some("2")) / new SummaryValue(Some(1)) shouldBe new SummaryValue(Some(2.0))
+ new SummaryValue(Some("2")) / new SummaryValue(Some(1.0)) shouldBe new SummaryValue(Some(2.0))
+ new SummaryValue(None) / new SummaryValue(Some(1.0)) shouldBe new SummaryValue(None)
+ }
+
+ @Test
+ def testLeft: Unit = {
+ new SummaryValue(Some(2.0)) % new SummaryValue(Some(1.0)) shouldBe new SummaryValue(Some(0))
+ new SummaryValue(Some(2.0)) % new SummaryValue(Some(1)) shouldBe new SummaryValue(Some(0))
+ new SummaryValue(Some(2)) % new SummaryValue(Some(1)) shouldBe new SummaryValue(Some(0))
+ new SummaryValue(Some("2")) % new SummaryValue(Some(1)) shouldBe new SummaryValue(Some(0))
+ new SummaryValue(Some("2")) % new SummaryValue(Some(1.0)) shouldBe new SummaryValue(Some(0))
+ new SummaryValue(None) % new SummaryValue(Some(1.0)) shouldBe new SummaryValue(None)
+ }
+
+}
+
+object SummaryValueTest {
+ val testSummary = Map(
+ "key_1" -> "test_1",
+ "samples" -> Map(
+ "sample1" -> Map(
+ "key_2" -> "test_2",
+ "libraries" -> Map(
+ "lib1" -> Map("key_3" -> "test_3")
+ )
+ )
+ )
+ )
+
+ val testSummaryFile = File.createTempFile("summary.", ".json")
+ testSummaryFile.deleteOnExit()
+
+ val writer = new PrintWriter(testSummaryFile)
+ writer.println(ConfigUtils.mapToJson(testSummary).nospaces)
+ writer.close()
+}
diff --git a/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index 8d3e47bdd9182a24d493c9083944f2fe98dc5287..d6b0f8c1d4f96a3c5af267341336cc8d0f2c452f 100644
--- a/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -58,7 +58,7 @@ class Carp(val root: Configurable) extends QScript with MultisampleMappingTrait
override def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends super.Sample(sampleId) {
- override def preProcessBam = Some(createFile(".filter.bam"))
+ override def preProcessBam = Some(createFile("filter.bam"))
val controls: List[String] = config("control", default = Nil)
diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
index c38cb8564ddb0f9243443bab60f6cb41ceec5b53..4f84d061198ee9449811cd414c72e661ee1e501b 100644
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
@@ -73,7 +73,7 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
/** Variantcallers requested by the config */
protected val configCallers: Set[String] = config("variantcallers")
- protected val callers: List[Variantcaller] = {
+ val callers: List[Variantcaller] = {
(for (name <- configCallers) yield {
if (!callersList.exists(_.name == name))
Logging.addError(s"variantcaller '$name' does not exist, possible to use: " + callersList.map(_.name).mkString(", "))
diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
index 2f7b8446b4c0a64b1348edb396f43fedcaaab4d3..a08703e95dc4ce61437641df80dd3c8da1641394 100644
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
@@ -13,14 +13,21 @@ class HaplotypeCallerGvcf(val root: Configurable) extends Variantcaller {
val name = "haplotypecaller_gvcf"
protected def defaultPrio = 5
+ /**
+ * Map of sample name -> gvcf. May be empty.
+ */
+ protected var gVcfFiles: Map[String, File] = Map()
+
+ def getGvcfs = gVcfFiles
+
def biopetScript() {
val gvcfFiles = for ((sample, inputBam) <- inputBams) yield {
val hc = gatk.HaplotypeCaller.gvcf(this, inputBam, new File(outputDir, sample + ".gvcf.vcf.gz"))
add(hc)
- hc.out
+ sample -> hc.out
}
- val genotypeGVCFs = gatk.GenotypeGVCFs(this, gvcfFiles.toList, outputFile)
+ val genotypeGVCFs = gatk.GenotypeGVCFs(this, gvcfFiles.values.toList, outputFile)
add(genotypeGVCFs)
}
}
diff --git a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala
index a2e13a46602dc9ea6bee2b3cfd19e2c251d8f905..c484171187fc31c27a06c7bd69d10433c9a9bb86 100644
--- a/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala
+++ b/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala
@@ -28,6 +28,9 @@ trait Variantcaller extends QScript with BiopetQScript with Reference {
var namePrefix: String = _
+ /**
+ * Map of samplename -> (preprocessed) bam file
+ */
var inputBams: Map[String, File] = _
def init() = {}
diff --git a/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala b/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
index eb1d40ece24ce6862023eae3343b84c840ea3e42..976fa91996d820ff38fcf22357a358f46277a848 100644
--- a/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+++ b/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
@@ -58,7 +58,9 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
def multisampleCalling: Boolean = true
def sampleCalling = false
def libraryCalling = false
- def dbsnp: Boolean = true
+ def dbsnp = true
+ def svCalling = false
+ def annotation = false
@Test(dataProvider = "shivaOptions")
def testShiva(f: String, sample1: Boolean, sample2: Boolean,
@@ -73,7 +75,9 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
"single_sample_variantcalling" -> sampleCalling,
"library_variantcalling" -> libraryCalling,
"use_indel_realigner" -> realign,
- "use_base_recalibration" -> baseRecalibration), m)
+ "use_base_recalibration" -> baseRecalibration,
+ "sv_calling" -> svCalling,
+ "annotation" -> annotation), m)
}
@@ -96,6 +100,21 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
pipeline.functions.count(_.isInstanceOf[BaseRecalibrator]) shouldBe (if (dbsnp && baseRecalibration) (numberLibs * 2) else 0)
pipeline.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration) numberLibs else 0)
+ pipeline.summarySettings.get("annotation") shouldBe Some(annotation)
+ pipeline.summarySettings.get("sv_calling") shouldBe Some(svCalling)
+
+ pipeline.samples foreach {
+ case (sampleId, sample) =>
+ sample.summarySettings.get("single_sample_variantcalling") shouldBe Some(sampleCalling)
+ sample.summarySettings.get("use_indel_realigner") shouldBe Some(realign)
+ sample.libraries.foreach {
+ case (libId, lib) =>
+ lib.summarySettings.get("library_variantcalling") shouldBe Some(libraryCalling)
+ lib.summarySettings.get("use_indel_realigner") shouldBe Some(realign)
+ lib.summarySettings.get("use_base_recalibration") shouldBe Some(baseRecalibration && dbsnp)
+ }
+ }
+
pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (
(if (multisampleCalling) 2 else 0) +
(if (sampleCalling) numberSamples * 2 else 0) +
@@ -125,6 +144,20 @@ class ShivaSampleCallingTest extends ShivaTestTrait {
override def baseRecalibrationProvider = Array(false)
override def sampleCalling = true
}
+class ShivaWithSvCallingTest extends ShivaTestTrait {
+ override def sample1 = Array(true)
+ override def sample2 = Array(false)
+ override def realignProvider = Array(false)
+ override def baseRecalibrationProvider = Array(false)
+ override def svCalling = true
+}
+class ShivaWithAnnotationTest extends ShivaTestTrait {
+ override def sample1 = Array(true)
+ override def sample2 = Array(false)
+ override def realignProvider = Array(false)
+ override def baseRecalibrationProvider = Array(false)
+ override def annotation = true
+}
object ShivaTest {
val outputDir = Files.createTempDir()
@@ -170,7 +203,18 @@ object ShivaTest {
"wigtobigwig" -> Map("exe" -> "test"),
"md5sum" -> Map("exe" -> "test"),
"bgzip" -> Map("exe" -> "test"),
- "tabix" -> Map("exe" -> "test")
+ "tabix" -> Map("exe" -> "test"),
+ "breakdancerconfig" -> Map("exe" -> "test"),
+ "breakdancercaller" -> Map("exe" -> "test"),
+ "pindelconfig" -> Map("exe" -> "test"),
+ "pindelcaller" -> Map("exe" -> "test"),
+ "pindelvcf" -> Map("exe" -> "test"),
+ "clever" -> Map("exe" -> "test"),
+ "delly" -> Map("exe" -> "test"),
+ "pysvtools" -> Map(
+ "exe" -> "test",
+ "exclusion_regions" -> "test",
+ "translocations_only" -> false)
)
val sample1 = Map(