From df5b8d8cc721fa6c4a8c385d6506b20f933a82c5 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 15 May 2016 19:19:13 +0200
Subject: [PATCH] Fixed tests
---
.../sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala | 4 ++--
.../biopet/pipelines/shiva/ShivaVariantcallingTest.scala | 6 +++---
2 files changed, 5 insertions(+), 5 deletions(-)
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 4f84d0611..d99948e4b 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
@@ -179,8 +179,8 @@ class ShivaVariantcalling(val root: Configurable) extends QScript
/** Settings for the summary */
def summarySettings = Map(
"variantcallers" -> configCallers.toList,
- "regions_of_interest" -> roiBedFiles.map(_.getName.stripSuffix(".bed")),
- "amplicon_bed" -> ampliconBedFile.map(_.getName.stripSuffix(".bed"))
+ "regions_of_interest" -> roiBedFiles.map(_.getName),
+ "amplicon_bed" -> ampliconBedFile.map(_.getAbsolutePath)
)
/** Files for the summary */
diff --git a/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala b/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
index 7d8fe1452..865c3cafc 100644
--- a/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+++ b/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
@@ -117,13 +117,13 @@ trait ShivaVariantcallingTestTrait extends TestNGSuite with Matchers {
(if (haplotypeCallerAllele) 1 else 0) + (if (haplotypeCallerGvcf) bams else 0)
pipeline.functions.count(_.isInstanceOf[UnifiedGenotyper]) shouldBe (if (unifiedGenotyper) 1 else 0) +
(if (unifiedGenotyperAllele) 1 else 0)
- pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (1 + callers.size + (roiBedFiles ++ ampliconBedFile).length)
+ pipeline.functions.count(_.isInstanceOf[VcfStats]) shouldBe (1 + callers.size + (roiBedFiles ++ ampliconBedFile).length * (1+ callers.size))
pipeline.functions.count(_.isInstanceOf[VtNormalize]) shouldBe (if (normalize) callers.size else 0)
pipeline.functions.count(_.isInstanceOf[VtDecompose]) shouldBe (if (decompose) callers.size else 0)
- pipeline.functions.count(_.isInstanceOf[GenotypeConcordance]) shouldBe (if (referenceVcf.isDefined) 1 else 0)
+ pipeline.functions.count(_.isInstanceOf[GenotypeConcordance]) shouldBe (if (referenceVcf.isDefined) 1 + callers.size else 0)
pipeline.summarySettings.get("variantcallers") shouldBe Some(callers.toList)
- pipeline.summarySettings.get("amplicon_bed") shouldBe ampliconBedFile.map(_.getAbsolutePath)
+ pipeline.summarySettings.get("amplicon_bed") shouldBe Some(ampliconBedFile.map(_.getAbsolutePath))
pipeline.summarySettings.get("regions_of_interest") shouldBe Some(roiBedFiles.map(_.getAbsolutePath))
}
}
--
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