From 62308c50c51355e53e2a598f91208e0f4c5f929f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 12 Feb 2015 21:16:02 +0100
Subject: [PATCH] Added star-2pass and stampy to data provider, not having 192
unit tests
---
.../nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
index cd4eaea9b..525382c5a 100644
--- a/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+++ b/public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
@@ -32,7 +32,7 @@ class MappingTest extends TestNGSuite with Matchers {
@DataProvider(name = "mappingOptions", parallel = true)
def mappingOptions = {
- val aligners = Array("bwa", "bwa-aln", "star", "bowtie")
+ val aligners = Array("bwa", "bwa-aln", "star", "star-2pass", "bowtie", "stampy")
val paired = Array(true, false)
val chunks = Array(1, 5, 10, 100)
val skipMarkDuplicates = Array(true, false)
@@ -77,7 +77,6 @@ class MappingTest extends TestNGSuite with Matchers {
mapping.functions.count(_.isInstanceOf[BwaAln]) shouldBe ((if (aligner == "bwa-aln") (if (paired) 2 else 1) else 0) * chunks)
mapping.functions.count(_.isInstanceOf[BwaSampe]) shouldBe ((if (aligner == "bwa-aln") (if (paired) 1 else 0) else 0) * chunks)
mapping.functions.count(_.isInstanceOf[BwaSamse]) shouldBe ((if (aligner == "bwa-aln") (if (paired) 0 else 1) else 0) * chunks)
- mapping.functions.count(_.isInstanceOf[Star]) shouldBe ((if (aligner == "star") 1 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[Star]) shouldBe ((if (aligner == "star") 1 else if (aligner == "star-2pass") 3 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[Bowtie]) shouldBe ((if (aligner == "bowtie") 1 else 0) * chunks)
mapping.functions.count(_.isInstanceOf[Stampy]) shouldBe ((if (aligner == "stampy") 1 else 0) * chunks)
@@ -109,7 +108,7 @@ object MappingTest {
"bwa" -> Map("exe" -> "test"),
"star" -> Map("exe" -> "test"),
"bowtie" -> Map("exe" -> "test"),
- "stampy" -> Map("exe" -> "test"),
+ "stampy" -> Map("exe" -> "test", "genome" -> "test", "hash" -> "test"),
"samtools" -> Map("exe" -> "test")
)
}
\ No newline at end of file
--
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