Commit 6f78cb16 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub

Merge pull request #76 from biopet/fix-BIOPET-655

Adding a printreads tests
parents b031a6e7 dc1777d2
......@@ -62,6 +62,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
def svCalling = false
def cnvCalling = false
def annotation = false
def usePrintReads = true
private var dirs: List[File] = Nil
......@@ -83,7 +84,8 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
"use_base_recalibration" -> baseRecalibration,
"sv_calling" -> svCalling,
"cnv_calling" -> cnvCalling,
"annotation" -> annotation), m)
"annotation" -> annotation,
"use_printreads" -> usePrintReads), m)
}
......@@ -105,7 +107,7 @@ trait ShivaTestTrait extends TestNGSuite with Matchers {
pipeline.functions.count(_.isInstanceOf[IndelRealigner]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
pipeline.functions.count(_.isInstanceOf[RealignerTargetCreator]) shouldBe (numberLibs * (if (realign) 1 else 0) + (if (sample2 && realign) 1 else 0))
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.functions.count(_.isInstanceOf[PrintReads]) shouldBe (if (dbsnp && baseRecalibration && usePrintReads) numberLibs else 0)
pipeline.summarySettings.get("annotation") shouldBe Some(annotation)
pipeline.summarySettings.get("sv_calling") shouldBe Some(svCalling)
......@@ -143,6 +145,10 @@ class ShivaNoDbsnpTest extends ShivaTestTrait {
override def realignProvider = Array(true)
override def dbsnp = false
}
class ShivaNoPrintReadsTest extends ShivaTestTrait {
override def realignProvider = Array(false)
override def usePrintReads = false
}
class ShivaLibraryCallingTest extends ShivaTestTrait {
override def sample1 = Array(true, false)
override def sample2 = Array(false, true)
......
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